a52ddf8759
patch 29Jun18
2018-06-30 08:03:24 -06:00
0f71ed1fec
Merge pull request #983 from akohlmey/python-module-typo
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fix typo in python module
2018-06-29 17:23:45 -06:00
43ffee980d
fix typo in python module
2018-06-29 19:07:14 -04:00
560b34aad0
Merge pull request #982 from lammps/doc-tweak-again
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couple more doc tweaks - sigh
2018-06-29 16:35:46 -06:00
ea35235ca0
couple more doc tweaks - sigh
2018-06-29 16:12:25 -06:00
474b59a1f3
Merge pull request #981 from lammps/latte-tweak
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fix glitch in ABIVERSION in fix latte
2018-06-29 16:03:45 -06:00
c63d77d0b8
Merge pull request #980 from lammps/spin-doc
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added SPIN package to Section_packages doc
2018-06-29 15:26:36 -06:00
bf9646cbbe
fix glitch in ABIVERSION in fix latte
2018-06-29 15:08:19 -06:00
d2dd76e655
added SPIN package to Section_packages doc
2018-06-29 14:56:27 -06:00
d649a6fe38
Merge pull request #979 from rbberger/small-python-fix
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Fixes issue #975
2018-06-29 14:55:25 -06:00
a8b7153f4e
Fixes issue #975
2018-06-29 16:03:38 -04:00
c3fe26a614
Merge pull request #977 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2018-06-29 13:57:14 -06:00
bbe77e4c31
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2018-06-29 15:33:23 -04:00
b819018084
Revert change to CMakeLists.txt which only works with 3.9+
2018-06-29 15:31:15 -04:00
6900f9edf9
Merge branch 'master' into collected-small-changes
2018-06-29 14:59:02 -04:00
11a8d4e1c3
Merge pull request #978 from lammps/new-makefiles
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new ARM makefiles, also some doc tweaks
2018-06-29 12:53:58 -06:00
d9396df5b9
Merge pull request #976 from akohlmey/collected-cmake-changes
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Collected cmake changes
2018-06-29 12:53:18 -06:00
0e047f2786
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2018-06-29 12:05:28 -04:00
ec99b0957c
new ARM makefiles, also some doc tweaks
2018-06-29 08:06:51 -06:00
75a3968039
multiple small tweaks to compute entropy/atom
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- improve error detection and messages
- avoid sigma/cutoff to be zero (and thus division by zero)
- move new/delete of temporary storage outside of loop
2018-06-29 06:48:11 -04:00
a3a2981cd2
remove unused class member
2018-06-29 01:22:35 -04:00
4f9c0456e6
eliminate variable length arrays from compute entropy/atom
2018-06-29 01:22:26 -04:00
ad4720ef00
make various compiler instrumentation flags "advanced" options
2018-06-29 01:00:20 -04:00
946bca82c5
add options to support GNU gcc sanitizers
2018-06-29 00:56:35 -04:00
85d7f7ddc9
Merge branch 'cmake_presets' of https://github.com/rbberger/lammps into collected-cmake-changes
2018-06-29 00:23:52 -04:00
ee0e9f94f1
Merge branch 'cmake_misc' of https://github.com/junghans/lammps into collected-cmake-changes
2018-06-29 00:16:19 -04:00
9f1aabea50
Merge branch 'cmake-fix-check-for-installed' of https://github.com/akohlmey/lammps into collected-cmake-changes
2018-06-29 00:13:23 -04:00
b3bc5fd823
Merge branch 'record-compile-flags' of https://github.com/akohlmey/lammps into collected-cmake-changes
2018-06-29 00:09:51 -04:00
e0dc53ab3f
Simplify CreateStyleHeader CMake utility
2018-06-28 14:22:37 -04:00
206d349d5b
Simplify DetectBuildSystemConflict CMake utility
2018-06-28 14:16:56 -04:00
4d629872d8
CMake preset docs wording
2018-06-28 14:05:25 -04:00
7a783870e2
Merge remote-tracking branch 'origin/master' into cmake_misc
2018-06-28 11:19:54 -06:00
0df8587c18
cmake: make GPU_ARCH free form
2018-06-28 11:13:51 -06:00
ad3d049edd
Merge pull request #974 from akohlmey/moltemplate-2.8.6
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Update moltemplate tool to version 2.8.6
2018-06-28 07:34:52 -06:00
7abc960d39
import moltemplate 2.8.6 from andrew jewett
2018-06-28 08:18:35 -04:00
23fb0370a9
Update CMake documentation
2018-06-28 00:39:24 -04:00
a043ddcb82
Merge branch 'master' into cmake_misc
2018-06-27 21:12:25 -04:00
a2b2507121
cmake: remove ENABLE_ALL option
2018-06-27 19:02:10 -06:00
6bd5a3d69b
Merge pull request #935 from julient31/spin_origin
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Spin origin
2018-06-27 16:58:27 -06:00
086e83456b
Merge pull request #970 from jrgissing/bond/react-optional-EdgeIDs
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Bond/react: edge IDs optional
2018-06-27 16:52:41 -06:00
1db4705a3d
Merge pull request #966 from wmbrownIntel/user-intel-2018Jun
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Intel Package: Bug fix when using LRT with minimize and for virial calculation with GNU...
2018-06-27 16:52:16 -06:00
8e77be0848
Merge pull request #967 from lammps/latte-tweak2
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small changes to last LATTE PR, including xControl to upper case
2018-06-27 16:44:25 -06:00
fc3694189e
update CODEOWNERS file for LATTE
2018-06-27 17:01:49 -04:00
75aacfd17f
add explanation comment to ABIVERSION define
2018-06-27 16:58:58 -04:00
08552fefe9
add md5 checksum support to Install.py for LATTE
2018-06-27 16:52:28 -04:00
20fe0cd9d0
Define CMake presets
2018-06-27 16:41:10 -04:00
8f4b7161c5
README: add cmake
2018-06-27 14:12:34 -06:00
38cdc1828d
insert spin package into make and cmake build system
2018-06-27 15:29:24 -04:00
9353569d30
cmake: add KOKKOS_ARCH to summary
2018-06-27 13:25:56 -06:00
868f5711a2
cmake: fix summary for GPU
2018-06-27 13:23:35 -06:00
7ffab9a228
cmake: added INJECT_KNL_FLAG option
2018-06-27 13:22:22 -06:00
58559d9e62
update src/.gitignor for SPIN package sources
2018-06-27 14:08:54 -04:00
3eed23d3f7
whitespace cleanup
2018-06-27 14:07:09 -04:00
d3b83885d1
make SPIN package examples consistent with other examples and add reference logs
2018-06-27 14:06:56 -04:00
3549345830
whitespace cleanup
2018-06-27 12:30:19 -04:00
244963aa19
fix incorrect scaling of emag bug
2018-06-27 12:29:34 -04:00
264f832b18
fix formatting of dump_modify docs
2018-06-27 07:58:57 -04:00
5c4bf8ac47
bond/react: optional EdgeIDs take2
2018-06-26 20:40:02 -06:00
6008cee6aa
...and replace with symbolic links
2018-06-26 16:02:56 -04:00
f33a2c982c
remove redundant potential files
2018-06-26 16:01:54 -04:00
8e14143908
Merge pull request #925 from PabloPiaggi/pair_entropy
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Pair entropy fingerprint
2018-06-26 13:16:09 -06:00
e6ef8ce5ee
Merge pull request #968 from oywg11/github-tutorial-update
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New paramteters for potential #839
2018-06-26 13:14:22 -06:00
ebe622ff7d
make edge atoms optional
2018-06-26 09:35:38 -06:00
f94cdf856c
Merge pull request #18 from lammps/master
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rebase
2018-06-26 10:15:52 -05:00
e2622f0230
Remap the paragraph
2018-06-26 17:27:55 +03:00
e4dd6dec40
Refine the documentation
2018-06-26 16:36:16 +03:00
b0126dd9d6
updata potential file CH.KC
2018-06-26 16:09:42 +03:00
f36e1a2cdc
Changed default deltabin from 2 to 3
2018-06-26 13:06:04 +02:00
c9d147c366
New paramteters for potential #839
2018-06-26 11:09:48 +03:00
19f81e0802
Add library functions for accessing LAMMPS configuration
2018-06-25 23:56:18 -04:00
49a91db0b2
small changes to last LATTE PR, including xControl to upper case
2018-06-25 17:43:31 -06:00
bad750eb2b
move LATTE ABI version constant into a define at the top of fix latte, as suggested by @sjplimp
2018-06-25 19:34:10 -04:00
5e48565761
Merge pull request #961 from cnegre/newsystem
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Added newsystem flag to be passed to latte
2018-06-25 17:20:57 -06:00
af91f7fa5d
LAMMPS does not build on windows without this one
2018-06-25 18:13:41 -04:00
0cd86bab22
Added new checksum value
2018-06-25 14:58:49 -06:00
bec82e4045
Added new checksum value
2018-06-25 14:23:44 -06:00
06b3209ad8
Commit JT 062518
2018-06-25 09:56:39 -06:00
2fd45050cd
Merge branch 'newsystem' of https://github.com/cnegre/lammps into newsystem
2018-06-25 08:44:57 -06:00
8ffa96c9e9
Added fix latte
2018-06-25 08:43:00 -06:00
6a9251245c
update MD5 sum for latte-v1.2.0.tar.gz src archive
2018-06-25 09:43:37 -04:00
cb2cf5b773
cmake: fixed comment
2018-06-25 06:31:09 -06:00
c4d0994d5e
cmake: fixed a typo
2018-06-25 06:29:24 -06:00
e2c03f0596
Simplify build system conflict checks
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- removes redundant code for conflict checks
- updates and expands original check to report fatal error instead of ignoring
files
- removes obsolete DetectAndRemovePackageHeader and RemovePackageHeader utility
functions which are no longer needed
- adds utility function DetectBuildSystemConflict, which loops over files and
reports an error if they exist in the lammps src directory.
- updates definition of LAMMPS_SOURCE_DIR, LAMMPS_LIB_SOURCE_DIR and
LAMMPS_LIB_BINARY_DIR to be absolute paths. This improves instructions in
error messages
2018-06-25 03:09:42 -04:00
9108306c11
Shorter entropy/atom example
2018-06-24 00:36:09 +02:00
86519ce213
Rename compute to entropy/atom
2018-06-24 00:25:07 +02:00
0b1d4a1696
liblammps.pc: fix lib suffix
2018-06-22 17:06:39 -06:00
264e4fd3b1
cmake: fix for <cmake-3.4
2018-06-22 17:05:55 -06:00
d237625d2a
patch 22Jun18
2018-06-22 14:08:09 -06:00
ce0f3daad6
cmake: don't include quiet packages in summary
2018-06-22 11:43:52 -06:00
cb7b23e220
cmake: add BUILD_EXE option
2018-06-22 11:11:09 -06:00
3f17d33fbe
cmake: add BUILD_LIB option
2018-06-22 11:06:12 -06:00
510834cb7b
Merge pull request #960 from lammps/latte-tweak
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made latte.in compatible with v1.1.1 and updated log files
2018-06-22 10:18:19 -06:00
2165a2aa9b
Changed version on cmakelist and install.py
2018-06-22 10:04:20 -06:00
ac41cc2c9a
cmake: add GPU_PREC status output
2018-06-22 09:02:10 -06:00
f5f73b0172
Merge pull request #958 from ndtrung81/gpu-updates
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Bug fixes and updates to the GPU package
2018-06-22 08:52:20 -06:00
35f5a685f6
small change to preempt a possible merge conflict
2018-06-22 08:19:49 -04:00
62984c1de0
small tweaks: improve messages and comments
2018-06-22 08:02:17 -04:00
04d040b863
update make purge list and fix checking for styles and installed package files in cmake
2018-06-22 07:57:03 -04:00
92f0f19df6
make info config output of compile time defines consistent with lmp_<machine> -h
2018-06-22 07:26:33 -04:00
dcdc7877a4
make compile time output more consistent and complete
2018-06-22 07:05:09 -04:00
2f11f2d7b2
query compile time settings in Info class
2018-06-22 06:59:09 -04:00
e25b6c81ee
use a more conventional way to generate and include the lmpinstalledpkgs.h file
2018-06-22 06:58:31 -04:00
80cca7c4c1
make has_XXX_support functions static, so they can be called without having to create an instance of Info, which requires a fully instantiation of the LAMMPS and Pointers classes
2018-06-22 06:57:05 -04:00
2fe0eabc09
Intel Package: Bug fix when using LRT with minimize. Bug fix for virial calculation when using GNU compilers. Most of framework for adding hybrid support is now in place.
2018-06-22 01:52:55 -07:00
7da8e69b45
add code to create lmpinstalledpkgs.h file with cmake
2018-06-21 19:08:09 -04:00
e8e1349da4
make the list of installed packages a static const class member of the LAMMPS class
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through this change, the list of packages becomes accessible for the
library interface and the python wrapper, e.g. to check whether a
prerequisite packages is installed (simpler/faster for quick highlevel
check than having to try instantiating a specific style).
2018-06-21 19:07:16 -04:00
dc132c8bf1
Added newsystem flag to be passed to latte
2018-06-21 15:40:20 -06:00
f0a2c57401
Merge pull request #959 from rbberger/cmake_documentation
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Expand cmake documentation
2018-06-21 13:57:48 -06:00
4ca3d30db7
Add BUILD_MPI and BUILD_OMP in cmake docs
2018-06-21 14:45:00 -04:00
cbfb751e92
made latte.in compatible with v1.1.1 and updated log files
2018-06-21 11:10:29 -06:00
65c895721f
Update README.md to reflect change ENABLE_* to PKG_*
2018-06-21 12:32:46 -04:00
bfacfc46be
Add TOC to README.md
2018-06-21 12:32:46 -04:00
919d95d375
Fill in package descriptions
2018-06-21 12:32:46 -04:00
258185690d
Fixup GitHub markup version
2018-06-21 12:32:46 -04:00
cea0227f14
Expand CMake build documentation
2018-06-21 12:32:32 -04:00
3e58ebea4f
Merge pull request #957 from akohlmey/collected_small_fixes
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Collected small changes and bugfixes for next patch release
2018-06-21 08:49:18 -06:00
7a22612bea
Merge pull request #956 from cnegre/latte_examples
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Added boxrel example and simplified latte.in
2018-06-21 08:48:56 -06:00
9805b5d34a
Merge pull request #955 from junghans/fortran_linking
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cmake: implicit fortran libs need to linked last
2018-06-21 08:48:26 -06:00
9f3cb83fb3
use a list instead of a string to store the names of installed packages
2018-06-20 17:57:17 -04:00
9f3fae1c47
record 3d-FFT array packaging algorithm
2018-06-20 17:23:37 -04:00
0e603493af
fix bug that made compilation fail with no packages installed
2018-06-20 17:23:37 -04:00
7f0c88c74b
refactor the gathering of compile time settings after discussion with @sjplimp
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- remove feature to record the compilation time and date
- remove 'echo -n' based "progress bar"
- update output format for "lmp_machine -h" to be consistent with help output
- move generation of lmpinstalledpkgs.h to be a separate target depending on
all sources and headers in src folder. this way it is only regenerated
when files are modified or packages installed
2018-06-20 17:23:37 -04:00
1f770a6a8f
print information about serial/parallel and MPI version for known libraries
2018-06-20 17:23:37 -04:00
596acaf4d2
give visual feedback on when the compile starts since gathering the package information can take time
2018-06-20 17:23:37 -04:00
472a1a501d
add lmpinstalledpks.h to the list of purgable files
2018-06-20 17:23:37 -04:00
eb485afc45
fix logic bug that would not create lmpinstalledpkgs.h when there was none
2018-06-20 17:23:37 -04:00
4265e68ff8
record installed packages
2018-06-20 17:23:37 -04:00
90f0586c9e
include compilation date as an example for embedding info, that is not a define
2018-06-20 17:23:37 -04:00
c371ce1005
include date when LAMMPS was compiled
2018-06-20 17:23:37 -04:00
e3a528a493
report compile time options (-DLAMMPS_XXX) in help output and info config
2018-06-20 17:23:37 -04:00
28504e91c0
Added missing source files for born/coul/wolf/cs in the gpu library
2018-06-20 15:08:24 -05:00
47482afbc1
add more thorough checks on parsing reaxff force field and signal when the lgvdw setting is correct.
2018-06-20 15:47:32 -04:00
7d3a549de9
remove entries that are not compatible with lgvdw yes and not included in the publication
...
closes #876
2018-06-20 14:16:34 -04:00
a9b794b2ab
Updates to the core-shell gpu pair styles
2018-06-20 10:43:13 -05:00
3ae8fdccd8
Updated the kernels for born/coul/long/cs and coul/long/cs gpu styles
2018-06-19 16:22:00 -05:00
70a7b37614
Updated pair coul/long/cs and born/coul/long/cs; updated gpu neighbor builds to support core-shell styles where r2 can be tiny.
2018-06-19 15:50:02 -05:00
036647c102
correct sign of virial tally in fix smd. issue reported by Dinesh SD on lammps-users
2018-06-19 16:19:37 -04:00
37b901eadb
Added boxrel example and simplified latte.in
2018-06-19 11:12:28 -06:00
4a88f53d22
adjust input files for changed paths
2018-06-18 19:17:25 -04:00
d4861e71d2
integrate SPIN package into documentation, fix links and make it consistent
2018-06-18 18:36:30 -04:00
5a3ef99272
cmake: implicit fortran libs need to linked last
2018-06-18 16:11:31 -06:00
605b4dca22
fix overlooked merge conflict
2018-06-18 18:09:59 -04:00
dade67664d
restore bugfix for refrences
2018-06-18 18:07:26 -04:00
93d6510d34
restore deleted file
2018-06-18 18:02:40 -04:00
4f8d1893e9
restore fix for formatting cleanup
2018-06-18 18:01:28 -04:00
7c7a80b31a
restore deleted file
2018-06-18 17:59:22 -04:00
da5931d65d
whitespace cleanup
2018-06-18 17:55:12 -04:00
83ae0ad26f
remove unused code
2018-06-18 17:47:59 -04:00
b189a328ed
source code formatting cleanups
2018-06-18 17:00:23 -04:00
469b67a39b
remove bogus file
2018-06-18 17:00:01 -04:00
1d0773d10d
remove redundant statement
2018-06-18 16:50:24 -04:00
03a7d1cd5d
Merge pull request #933 from rtoijala/fix_dt_reset_energy
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Limit atom energy change in fix dt/reset
2018-06-18 13:43:03 -06:00
08331da93d
Merge pull request #950 from martok/subst-equal-fmt
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Add support for inline format strings to immediate variable substitution
2018-06-18 13:42:24 -06:00
ab0f3debeb
Merge pull request #948 from martok/variable-string
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Variable style 'string' substitutes variables in definition
2018-06-18 10:50:36 -06:00
fe14bfd1d2
Merge pull request #951 from martok/meam-diaref-fix
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Apply modifications to MEAM & MEAM/C as found by Kyung-Han Kang
2018-06-18 10:29:57 -06:00
d55c7039ee
Merge pull request #943 from Pakketeretet2/improve-manifoldforce-warning
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Improve fix manifoldforce warning
2018-06-18 10:09:18 -06:00
87dcef7115
Merge pull request #952 from rbberger/coverage
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Add code coverage target to CMake
2018-06-18 10:08:31 -06:00
7e234497ff
Merge pull request #953 from jrgissing/bond/react-update
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Bond/react update
2018-06-18 10:08:06 -06:00
277b43b2fd
Merge pull request #949 from jdevemy/master
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Fix the tail correction with pair_nm
2018-06-18 10:07:26 -06:00
6f61ed2af5
Merge pull request #938 from akohlmey/collected-bugfixes
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Collected bugfixes and updates
2018-06-18 10:06:55 -06:00
16cc613993
Merge pull request #920 from junghans/mscg
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cmake: add DOWNLOAD_MSCG option
2018-06-18 10:06:16 -06:00
6842a527e0
Fixed bugs and added born/coul/long/cs/gpu and coul/long/cs/gpu, need tests
2018-06-18 00:15:28 -05:00
d094bf789c
Updated GPU/Install.sh
2018-06-17 11:50:41 -05:00
3750e0a427
resolve newton setting and parallel disparities, improve syntax error catching
2018-06-16 11:13:52 -06:00
40c4461a78
Merge pull request #17 from lammps/master
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rebase
2018-06-15 23:26:01 -06:00
d830fc2301
Inline find_program() for gcovr
2018-06-16 00:40:10 -04:00
265b6c261e
Fixed bugs with lj/expand/coul/long and its gpu version
2018-06-15 23:38:37 -05:00
3411b0e576
add more code owners
2018-06-15 18:03:15 -04:00
47458f1ca0
Add code coverage target to CMake
2018-06-15 17:57:33 -04:00
c4bcb7e73d
mention requirement to come after the box creation in Restrictions section
2018-06-15 17:52:54 -04:00
18b543179c
fix typo
2018-06-15 17:47:23 -04:00
14c4438a72
update docs to reflect the state of reserving space for topology info with molecule files
2018-06-15 17:46:09 -04:00
acd20512f0
require that box is defined before molecule command is issued
2018-06-15 17:40:14 -04:00
5fcdfe6dcb
describe the use of wildcards for adapting ranges of bond types
2018-06-15 17:35:43 -04:00
7c9afc1be2
change warning and move it do init() as discussed in PR #943
2018-06-15 17:27:23 -04:00
b2e6863d93
add reference log file.
2018-06-15 17:01:26 -04:00
cb887d48a1
include compute pentropy/atom in src/USER-MISC/README
2018-06-15 16:55:05 -04:00
9ef1bfe814
whitespace cleanup
2018-06-15 16:44:07 -04:00
76b85e4d25
rename source files for compute pentropy/atom to match the command name
2018-06-15 16:43:19 -04:00
8a2faff541
integrate compute pentropy/atom into the documentation tree
2018-06-15 16:40:25 -04:00
fe483a769f
update makefiles in lib/linalg to support .F files in addition to .f files
2018-06-15 15:35:34 -04:00
f312fbfe32
update Install.py to use a specific numbered release version instead of master
2018-06-15 15:16:10 -04:00
f68c6dddb8
Apply modifications to MEAM & MEAM/C as found by Kyung-Han Kang
2018-06-15 12:33:38 +02:00
c5b51df06e
Add support for inline format strings to immediate variable substitution
2018-06-14 14:17:37 +02:00
479cc9424d
C include
2018-06-14 13:57:10 +02:00
673202d05f
Bugfix for pair_nm and tail correction
2018-06-14 13:44:55 +02:00
3e79296dcf
Variable style 'string' substitutes variables in definition
2018-06-14 13:10:08 +02:00
fcf9ed0fc2
Merge pull request #946 from b-v/patch-1
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Update README.md
2018-06-13 13:01:15 -06:00
661848139c
Merge pull request #926 from ndtrung81/gpu-updates
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some updates to the GPU package
2018-06-13 12:57:01 -06:00
12d8370ec5
Update README.md
2018-06-12 23:03:33 +01:00
3c781afa6c
Switched to standard C++ header files for pair lj/expand/coul/long in USER-MISC
2018-06-09 09:41:03 -05:00
37268e435b
Merge remote-tracking branch 'origin/master' into mscg
2018-06-08 18:06:06 -06:00
29e555213c
Merge pull request #924 from junghans/cmake_misc
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miscellaneous CMake Fixes
2018-06-08 17:34:58 -06:00
965ac3cedd
cmake: lower cmake requirement to 2.8.12
2018-06-08 16:18:02 -06:00
30e3e9ab88
cmake: simplify Fortran linkage
2018-06-08 16:14:28 -06:00
6cb0c2e9c5
Merge pull request #937 from stanmoore1/kk_bonds
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Fix issues in Kokkos topology files
2018-06-08 15:42:40 -06:00
ebd93cac69
Merge pull request #930 from stanmoore1/kk_update
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Update Kokkos library to v2.7.00
2018-06-08 15:42:05 -06:00
a2dd21dca5
Made statement in if have equal whitespace on either side.
2018-06-08 15:15:37 -04:00
e78ed7d044
Improved the warning message of fix_manifoldforce about incompatible min_style.
2018-06-08 15:11:59 -04:00
142de878f9
Kokkos doesn't yet support map_style hash, so use may_style array by default if Kokkos is enabled
2018-06-08 09:38:16 -06:00
4c28827aa1
JT commit 060518
2018-06-05 12:32:18 -06:00
5a383aa518
Reverted fix nve/manifold/rattle to upstream.
2018-06-04 12:26:26 -04:00
a4a3133b76
Switched to standard C++ header files for consistency with other source files
2018-06-01 23:13:49 -05:00
9dda907f7d
Commit JT 060118 Changes Stan
2018-06-01 15:19:27 -06:00
fa5ecf88a5
change error->all to error->warning on pair style restartinfo bug
2018-06-01 16:13:05 -04:00
7ca794beb9
whitespace cleanup
2018-06-01 16:11:43 -04:00
c386bdddf9
Merge branch 'master' of https://www.github.com/lammps/lammps
2018-06-01 10:44:11 -04:00
56c3a0be29
support virtualenv on machines with python3 where it is called virtualenv-3
2018-05-31 19:03:28 -04:00
cf3095e938
document restartinfo bug message, add check to Pair::write_restart as well
2018-05-31 19:02:03 -04:00
6056c1db4d
fix restart bug in pair style quip
2018-05-31 18:54:38 -04:00
38182dcc60
clarify docs on what energy is monitored
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changes to the energy only consider the kinetic energy, so make that explicit in the augmented `fix dt/reset` docs
2018-05-31 17:32:19 -04:00
ef3c0dbf7b
Merge branch 'molecule-template-validity-checks' of https://github.com/jrgissing/lammps into collected-bugfixes
2018-05-31 16:30:25 -04:00
4c18a07193
Merge branch 'fix/adapt-wildcard-bondtypes' of https://github.com/jrgissing/lammps into collected-bugfixes
2018-05-31 16:15:33 -04:00
e3e040227b
Fix issues in Kokkos topology files
2018-05-30 12:31:20 -06:00
f2a6aa249f
Commit2 JT 052918: doc
2018-05-29 17:18:45 -06:00
6457e5eedb
Commit1 JT 052918 modifs files
2018-05-29 14:51:21 -06:00
c27e617fd8
Add logic to Makefile.kokkos
2018-05-29 11:33:18 -06:00
b9a8f91753
Limit atom energy change in fix dt/reset
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Allow limiting of the maximum energy change of an atom in
fix dt/reset in addition to the existing distance limit.
Useful especially for high-energy irradiation.
2018-05-28 10:57:40 +03:00
95e259fe71
also include consistent type checks
2018-05-26 15:18:26 -06:00
69a9f1bf94
molecule templates sanity checks
2018-05-26 15:03:24 -06:00
e7773808a5
Merge pull request #14 from lammps/master
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rebase
2018-05-26 14:38:13 -06:00
0368202d12
Merge pull request #929 from stanmoore1/snap_fix
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Small bugfixes for Pair Snap
2018-05-26 14:07:19 -06:00
3ba87e52e9
fix/adapt wildcard bondtypes
2018-05-25 21:18:11 -06:00
1422b0413b
Update Kokkos library to v2.7.00
2018-05-25 15:00:53 -06:00
18c6d7f289
Fix possible MPI deadlock in pair_snap
2018-05-24 15:31:49 -06:00
1b4068b575
Restore workaround for compiler bug in pair_snap.h
2018-05-24 15:31:22 -06:00
5f0e6d0aa7
Commit JT2 052418
2018-05-24 12:55:39 -06:00
99f4274483
Commit JT 052418 rm comments
2018-05-24 06:59:40 -06:00
341fa160fe
Updated UCL_Device built with OpenCL to use platforms that support accelerators by default
2018-05-23 16:11:55 -05:00
102be8dd8b
Commit JT 052318
2018-05-23 11:23:39 -06:00
6c42c9b378
Add missing OCL_TUNE define to CMake build
2018-05-22 20:21:58 -04:00
ce4a446cea
Merge pull request #911 from akohlmey/collected-small-changes
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Collected small changes and bugfixes
2018-05-22 10:11:12 -06:00
933cf92e36
Merge pull request #923 from akohlmey/remove-register
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Remove deprecated 'register' keyword
2018-05-22 10:02:32 -06:00
69903cb4aa
Merge pull request #921 from lammps/doctweaks
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tweaks to doc pages
2018-05-22 10:02:01 -06:00
6de4569483
Removed unused variables - corrected documentation
2018-05-22 17:29:51 +02:00
ad5cfb5ae6
Switched member variables from private to protected for lj/cut/dipole/long
2018-05-22 09:55:16 -05:00
fbc435a0cb
Formatted according to Lammps guidelines
2018-05-22 16:40:25 +02:00
108c31e24a
Moved to USER-MISC
2018-05-22 14:56:26 +02:00
e550f5120b
Updated docs
2018-05-22 12:44:40 +02:00
2f9e6d4566
Fixed bugs in lal_device.cpp with node_names dynamically allocated and dipole/long/gpu
2018-05-21 23:32:25 -05:00
1641f78e3e
Merge from lammps master
2018-05-21 16:06:53 -06:00
4ec31564fe
fix preprocessor directive bug in lib/atc
2018-05-21 16:50:16 -04:00
f5b7419108
fix typo reported in #915
2018-05-21 16:49:00 -04:00
1f193e02e0
update to c++ style include header syntax
2018-05-21 16:49:00 -04:00
838a1938bb
Added pair styles lj/expand/coul/long to USER-MISC and its gpu version to GPU package, added lj/cut/dipole/long/gpu; and added an example Makfile to build GPU package for multi-arch
2018-05-20 17:03:12 -05:00
df3eb36519
cmake: KOKKOS enables C++-11 internally
2018-05-20 08:22:20 -06:00
bb6dcb8ebd
cmake: make CORESHELL depend on KSPACE
2018-05-20 07:54:00 -06:00
e6f76451eb
cmake: fix pkg_depend macro
2018-05-20 07:27:22 -06:00
cfb350d40b
cmake: QMMM and H5MD need C
2018-05-19 11:07:19 -06:00
5daf1fe0d4
remove deprecated 'register' keyword. closes #922
2018-05-18 17:43:18 -04:00
2e7b919774
linalg: update to netlib lapack-3.7.1
2018-05-18 15:20:47 -06:00
858c211fdc
linalg: add functions needed for MSCG
2018-05-18 15:08:08 -06:00
6997aedf30
cmake: avoid warning of missing include dir
2018-05-18 15:06:54 -06:00
cab602045e
tweaks to doc pages
2018-05-18 08:37:29 -06:00
124641dc8a
Examples - new local option
2018-05-18 15:13:48 +02:00
6944973484
cmake: don't build Eigen3 for USER-SMD
2018-05-17 20:07:43 -06:00
9e82c86fbd
cmake: minor improvement for MSCG
2018-05-17 20:01:33 -06:00
68dd7d4f2b
cmake: fix 2 typos in MSCG build
2018-05-17 17:43:16 -06:00
b2da3ca3e9
cmake: add DOWNLOAD_MSCG option
2018-05-17 17:23:54 -06:00
e1361a9dca
Merge branch 'master' of https://www.github.com/lammps/lammps
2018-05-17 10:42:18 -04:00
94c6d2d546
Merge pull request #918 from stanmoore1/kk_atomics
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Fix performance regression in KOKKOS package
2018-05-16 16:46:02 -06:00
585a164e78
Merge pull request #901 from timattox/bugfix_atom_vec_dpd
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USER-DPD: bugfix for AtomVecDPD::unpack_restart() and the Kokkos version
2018-05-16 16:45:35 -06:00
5a4a7cebc1
Fix performance regression in KOKKOS package
2018-05-16 16:12:05 -06:00
133f0922b3
Merge branch 'master' of https://www.github.com/lammps/lammps
2018-05-15 12:58:40 -04:00
1a88ffd5ab
Updated fix_nve_manifold_rattle.cpp
2018-05-15 12:58:32 -04:00
307e471456
Merge pull request #914 from jrgissing/bond-react-restart
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smooth restarts with bond/react
2018-05-14 16:16:58 -06:00
f5d66e74c5
Merge pull request #913 from jrgissing/bond/react-doc-reformat
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Bond/react doc reformat
2018-05-14 16:16:46 -06:00
bebf25dcb3
Merge pull request #912 from ellio167/kim-update
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Update to kim-api-v1.9.5
2018-05-14 16:16:18 -06:00
3f316f71ef
Merge pull request #910 from junghans/cmake_intel
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USER-INTEL: enforce icc and add icc flags
2018-05-14 16:15:50 -06:00
8303d1a375
allow smooth restarts
2018-05-13 22:49:54 -06:00
363d8ef775
tweaks1
2018-05-13 15:45:43 -06:00
a449488b1d
simplify
2018-05-13 12:14:15 -06:00
e076d08ee9
correctly render doc page
2018-05-12 14:17:29 -06:00
1a5144bf37
Merge pull request #13 from lammps/master
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rebase
2018-05-12 12:59:57 -06:00
ca6920be72
Merge pull request #907 from akohlmey/dump_maxfile
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Implement 'dump_modify maxfiles' feature
2018-05-12 12:59:33 -06:00
55d8cc0341
cmake: add DOWNLOAD_KIM option
2018-05-12 09:48:15 -06:00
6b73e29f64
cmake: update kim to v1.9.5
2018-05-12 09:43:13 -06:00
09046ad3f7
Update to kim-api-v1.9.5
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Fixes the 'everything' option
2018-05-12 10:08:09 -05:00
06c18dd36c
cmake: make CMAKE_VERBOSE_MAKEFILE option visible
2018-05-11 17:50:50 -06:00
55bd823339
cmake: fix icc versioning
2018-05-11 17:48:31 -06:00
77e04a9213
Merge branch 'dump_maxfile' of github.com:akohlmey/lammps into dump_maxfile
2018-05-11 18:04:06 -04:00
233f03ea8e
windows portability bugfix
2018-05-11 18:03:49 -04:00
f65b06de0e
dump_modify maxfiles tweak
2018-05-11 15:54:16 -06:00
0f32d603b5
tweaks to dump_modify maxfiles doc page
2018-05-11 15:52:18 -06:00
3440b1a2a7
Merge pull request #909 from lammps/tablecut
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new dihedral table/cut command
2018-05-11 15:41:52 -06:00
8952b1107c
cmake: add user overwrite for USER-INTEL
2018-05-11 15:33:18 -06:00
b3b3c225e8
cmake: check that USER-INTEL flags actually work
2018-05-11 15:32:32 -06:00
4d34e55072
rename jpeg file, recreate tex file and fix typo in docs for dihedral style table/cut
2018-05-11 17:31:14 -04:00
437e854741
Commit JT 051118 before CEA
2018-05-11 15:24:26 -06:00
4820cef5d4
cmake: USER-INTEL fix flags
2018-05-11 15:19:29 -06:00
e7598eeec0
ignore new style sources in USER-MSIC
2018-05-11 16:17:00 -04:00
a5d29fa52e
Merge remote-tracking branch 'origin/master' into cmake_intel
2018-05-11 14:13:30 -06:00
821ef0cf77
update documentation for dihedral style table/cut
2018-05-11 16:08:23 -04:00
42f22a9723
Merge pull request #908 from akohlmey/coverity-scan-fixes
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Correct small bugs found by static code analysis
2018-05-11 14:06:18 -06:00
0d8110bc19
Merge pull request #903 from akohlmey/move-enums-to-headers
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Move enums that have to be consistent across files into a class
2018-05-11 14:05:58 -06:00
44c5e88e24
Merge pull request #902 from junghans/cmake
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CMake improvements
2018-05-11 14:05:26 -06:00
8d24101df4
patch 11May18
2018-05-11 14:04:49 -06:00
308dac6821
fix force->bounds() bug and remove dead code
2018-05-11 15:54:51 -04:00
944dab1351
USER-INTEL: enforce icc and add icc flags
2018-05-11 11:53:34 -06:00
c3cc07bd3d
truncate filename path to a segment starting with 'src/'
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this will trim warnings and error messages when compiling using the CMake
build system, which uses full paths. as a bonus,one can now see, if a
source is taken from a package or not.
2018-05-11 13:52:34 -04:00
c50258e89c
cmake: ENABLE -> PKG for packages
2018-05-11 07:51:59 -06:00
9674512997
new dihedral table/cut command
2018-05-11 07:36:40 -06:00
f864584bce
correct small bugs found by coverity scan static code analysis
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- in fix rigid, rigid/small, and poems, a string argument was
incorrectly assigned to a %d format
- plug two small memory leaks in fix bond/react
2018-05-11 00:43:09 -04:00
075598b405
port dump_modify maxfiles option to COMPRESS and MPIIO package
2018-05-10 23:44:27 -04:00
7780d92823
implement 'dump_modify maxfiles' feature as discussed
2018-05-10 23:25:26 -04:00
66caf1c1a3
cmake: rename PNG,JPEG options to WITH_*
2018-05-10 20:33:18 -06:00
95eb86d6c7
Need to use MPI_CXX_INCLUDE_PATH instead of MPI_C_INCLUDE_PATH on Fedora 28 with cmake 3.11
2018-05-10 21:20:06 -04:00
724ade0af3
silence compiler warnings about bool vs int in AtC lib
2018-05-10 18:48:47 -04:00
d43c556263
cmake: fix typo and added summary for KSPACE package
2018-05-10 16:11:10 -06:00
40a8b1af79
fix stupid bug in AtC when using alloca() instead of VLAs
2018-05-10 17:42:10 -04:00
33a41a4fb3
Merge pull request #906 from akohlmey/recover-jenkins
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Recover jenkins test builds
2018-05-10 15:20:01 -06:00
d7992f324d
cmake: summary, fix typo, more info
2018-05-10 14:30:45 -06:00
79d1d3458e
revive lib/atc/Makefile.mpic++
2018-05-10 15:44:36 -04:00
a25895d31d
cmake: add FFT_SINGLE option
2018-05-10 12:52:04 -06:00
4f762deff8
cmake: drop FFTW2 support
2018-05-10 12:37:11 -06:00
843f89fc92
cmake: add GPU into to summary
2018-05-10 12:36:09 -06:00
6336c3b975
cmake: add option to download voro
2018-05-10 12:31:55 -06:00
a43e74180a
cmake: add downlad option for LATTE
2018-05-10 11:09:15 -06:00
6626cd5aaa
cmake: add Eigen3 download for USER-SMD
2018-05-10 11:04:56 -06:00
aa1d815fe5
Merge pull request #904 from jrgissing/typing_bugfix
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Retyping parameters bugfix
2018-05-10 06:56:50 -06:00
863a85353a
type reassignment bugfix for edge atoms
2018-05-09 23:55:04 -06:00
662535865f
Merge pull request #12 from lammps/master
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rebase
2018-05-09 23:51:57 -06:00
6226ec8831
import enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER} from pair.h
2018-05-10 01:32:57 -04:00
6c91cc1f76
cmake: rename ENABLE_MPI to BUILD_MPI
2018-05-09 23:12:00 -06:00
4e42ee2cfc
cmake: add BUILD_OMP option
2018-05-09 23:09:23 -06:00
1224296365
move enum{INT,DOUBLE,STRING,BIGINT}; to Dump class in dump.h
2018-05-10 01:09:04 -04:00
25cef528c9
cmake: remove -fno-second-underscore injection
2018-05-09 23:03:22 -06:00
6359392834
cmake: MEAM needs a C compiler
2018-05-09 23:02:00 -06:00
71e1867dd2
move enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; to Comm class
2018-05-10 00:50:20 -04:00
f90af1839e
cmake: add a warning for QMMM
2018-05-09 22:42:33 -06:00
2ebd4eb26e
cmake: COMPRESS needs zlib
2018-05-09 22:24:22 -06:00
3682bc47c2
move enum{NO_REMAP,X_REMAP,V_REMAP} to Domain class in domain.h
2018-05-10 00:20:10 -04:00
2797afbf3e
cmake: only enable CXX by default
2018-05-09 22:16:19 -06:00
635383c00c
cmake: cache check for installed packages
2018-05-09 22:09:19 -06:00
b6a8168e3f
fix bug in procmap Comm::MULTIPLE import
2018-05-10 00:02:12 -04:00
71fce2e413
move enum{SINGLE,MULTI} and enum{MULTIPLE} to Comm in comm.h
2018-05-09 23:57:24 -04:00
994fd2af0e
move enum{NSQ,BIN,MULTI} to the Neighbor class in neighbor.h
2018-05-09 23:46:09 -04:00
d8138a5b4c
move enum{IGNORE,WARN,ERROR) into Thermo class and use Thermo:: namespace to reference it
2018-05-09 18:11:31 -04:00
a001f2c248
cmake: turn PNG, JPEG, GZIP and FFMPEG into options
2018-05-09 15:54:04 -06:00
8104568b6a
cmake: improve check again make-based build system
2018-05-09 15:26:59 -06:00
96d1c421df
cmake: improve summary
2018-05-09 15:19:52 -06:00
dde271db36
Merge pull request #900 from lammps/install
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Consistency tweaks to various package Install.sh files and related shell scripts
2018-05-09 15:10:35 -06:00
a7a83b118d
update dependencies for USER-CGSDK package. make script permissions consistent
2018-05-09 16:13:54 -04:00
8697cac6aa
make QEQ package depend on MANYBODY
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the qeq/fire style depends on pair style comb,
thus QEQ needs and explicit Install.sh file and
it has to depend on MANYBODY
2018-05-09 16:06:37 -04:00
96c5c92b1a
USER-DPD: bugfix for AtomVecDPD::unpack_restart() and the Kokkos version
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Also, cleaned up UCG_MASK and UCGNEW_MASK usage in atom_vec_dpd_kokkos.cpp
Fixes a crash when using the python interface on a 2nd LAMMPS invocation
when using the restart (or replicate) commands, because of garbage
in the uCG and uCGnew arrays leftover from the previous LAMMPS invocation.
2018-05-09 15:00:10 -05:00
793260f227
consistency tweak to package LATTE Install.sh file
2018-05-09 11:47:57 -06:00
e5a589e05a
Merge pull request #898 from robeme/fix_restrain_individual_energies
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Output individual energies in fix restrain
2018-05-09 11:43:52 -06:00
dc8e141501
Merge pull request #896 from akohlmey/cplusplus-compliance-lib
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C++ style header includes and C++ standard conforming code changes in lib folder
2018-05-09 11:43:03 -06:00
9f03a6798f
Merge pull request #880 from stanmoore1/kk_dep
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Remove Kokkos deprecated code
2018-05-09 11:41:25 -06:00
b4e5828a60
Update fix_restrain.cpp
2018-05-08 15:36:32 -04:00
671876efef
Make the description of global properties more explicit
2018-05-08 15:33:42 -04:00
8705ea9fc5
replace pointless use of strncat() emulating strcat() with plain strcat()
2018-05-08 08:49:05 -04:00
16697fc4cb
forgot to reduce energies
2018-05-08 10:46:41 +02:00
53fc9f1f0f
updated doc for new fix restrain output
2018-05-08 10:11:00 +02:00
6960529594
set appropriate flags for computing a vector in constructor of fix restrain
2018-05-08 10:02:10 +02:00
fccc16f42c
tune OpenCL for generic architecture by default
2018-05-08 00:50:23 -04:00
e7e1827e57
remove variable length arrays in gpu lib
2018-05-08 00:48:53 -04:00
c9817b0db9
update src/.gitignore
2018-05-08 00:33:27 -04:00
318dfd0613
correct indentation
2018-05-08 00:32:49 -04:00
f4d14c96e8
convert poems lib to use c++-style header includes
2018-05-08 00:29:56 -04:00
3394d18a2a
convert gpu lib to use c++-style include files
2018-05-08 00:25:10 -04:00
ff6507e7b7
convert colvars lib to use c++ style header files
2018-05-08 00:17:57 -04:00
fff962646f
convert awpmd header include to c++ style
2018-05-08 00:10:20 -04:00
f39a8d46d1
convert atc library header files to C++ style
2018-05-08 00:05:18 -04:00
00b92cd93b
Merge pull request #11 from lammps/master
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rebase
2018-05-07 21:58:57 -06:00
808eb2a25e
Merge pull request #895 from junghans/cmake
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cmake: remove obsolete BODY/POEMS conflict
2018-05-07 16:43:25 -06:00
1888b616c4
remove some extra semicolons
2018-05-07 18:04:25 -04:00
761b15b8f4
cmake: remove obsolete BODY/POEMS conflict
2018-05-07 16:03:23 -06:00
cde6e9b7c4
Fix CUDA issue in pair_exp6_rx_kokkos
2018-05-07 15:51:15 -06:00
104dde27ed
eliminate variable length arrays from AtC lib for C++ standard compliance
2018-05-07 17:36:34 -04:00
bfdfd36c1c
Merge pull request #894 from akohlmey/cplusplus-clang-fixes
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More fixes to conform with C++ standards as indicated by Clang
2018-05-07 14:53:43 -06:00
a4759210a8
Merge pull request #893 from ohenrich/user-cgdna
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Docs update and journal reference for USER-CGDNA package
2018-05-07 14:39:32 -06:00
7fed6c7e4c
Merge pull request #634 from craabreu/master
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Computation of forces/torques on rigid bodies moved to post_force
2018-05-07 14:39:10 -06:00
82217001c8
must use fabs() on doubles, not abs(), to avoid ambiguity
2018-05-07 15:56:35 -04:00
b2370b6986
use correct namespace when instantiating IntelBuffers;
2018-05-07 15:49:51 -04:00
624173d25a
Merge branch 'master' into kk_dep
2018-05-07 13:42:33 -06:00
7cf42e42eb
make links to citations unique across files 2/2
2018-05-07 14:25:18 -04:00
d80b375e26
make links to citations unique across files 1/2
2018-05-07 14:24:00 -04:00
d203118286
update rigid body reference outputs. add bodyforces early examples
2018-05-07 14:19:50 -04:00
74fbb84b8c
Merge pull request #878 from jrgissing/group_extract
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Group extract
2018-05-07 11:45:37 -06:00
5076b6d161
Removed old documentation
2018-05-07 18:25:55 +01:00
fcdcdb3286
Merge branch 'master' into user-cgdna
2018-05-07 18:19:24 +01:00
722549965e
Added reference to implementation paper
2018-05-07 18:13:18 +01:00
ca96a7ab05
Merge pull request #891 from akohlmey/collected-small-changes
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Collected small changes, fixes and updates
2018-05-07 10:43:19 -06:00
8ec033e823
Merge pull request #889 from akohlmey/cplusplus-compliance
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Collected changes to restore C++ standard compliance
2018-05-07 10:42:22 -06:00
a7c9418629
Merge pull request #890 from jrgissing/bond_react_final_touches
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bond/react final touches
2018-05-07 10:37:47 -06:00
bc0c405bfa
Merge pull request #887 from akohlmey/create-bonds-single-bugfix
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Fix bug in create_bonds single/bond
2018-05-07 10:37:00 -06:00
1ea5b9eabb
Merge pull request #879 from mdelyser/USER-BOCS
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USER-BOCS
2018-05-07 10:34:51 -06:00
d9d33ac766
add ability to set multiplicity for dihedrals with fix restrain
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this introduces an optional keyword, so backward compatibility is preserved.
this closes #884
2018-05-07 07:23:29 -04:00
d51745fd27
whitespace cleanup
2018-05-07 07:23:29 -04:00
c3588f08b7
provide keyword/value option to compute ackland/atom for selecting legacy or current variant of implementation
2018-05-07 07:23:29 -04:00
ecfe5c8373
use american spelling of neighbor consistently in docs and code comments
2018-05-07 07:23:29 -04:00
009666d9a5
need to ignore pair style kim in src/
2018-05-07 07:23:29 -04:00
551ea9694d
add VTK config for recent fedora versions
2018-05-07 07:23:29 -04:00
d7339bbd9e
significantly expand .github/CODEOWNERS file to automatically notify more contributors of changes to files/packages they maintain
2018-05-07 07:23:29 -04:00
934f825388
update USER-INTEL Install.sh script and dependency handling
2018-05-07 07:23:29 -04:00
f4fbdea0b3
update .gitignore for lib/latte
2018-05-07 07:23:29 -04:00
14588f6242
remove dead code and fix compilation for fix mscg
2018-05-07 07:23:29 -04:00
5e49976b70
correct typo in fix bond/react docs
2018-05-06 11:17:34 -04:00
9d9d7cb9ed
update example log files
2018-05-06 11:10:40 -04:00
941d289a69
cosmetic changes to avoid compiler warnings
2018-05-06 10:54:34 -04:00
e1f9ee1347
fix1
2018-05-06 01:04:23 -06:00
916ed71760
fix bond/react final touches
2018-05-06 00:34:03 -06:00
9d6891823a
some more cosmetic changes
2018-05-05 20:38:22 -04:00
e14b61e4a4
replace variable length array with constant length through making maxLine constant
2018-05-05 19:51:30 -04:00
2d321a602c
Merge pull request #10 from lammps/master
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rebase
2018-05-05 14:22:23 -06:00
9acd35abe2
another change to fix poems
2018-05-05 10:52:39 -06:00
0c53afbfcf
more changes to fix rigid and fix poems
2018-05-05 10:39:01 -06:00
2616dd91f9
include USER-BOCS package in cmake
2018-05-05 12:05:32 -04:00
f7c37a7a98
adapt isfinite() handling to upstream
2018-05-05 11:46:35 -04:00
095ca76b5b
plug memory leaks in USER-BOCS
2018-05-05 11:44:21 -04:00
f9f8e2bdbe
update USER-BOCS example to match LAMMPS style and include reference logs
2018-05-05 11:43:05 -04:00
735bceb468
Merge branch 'master' into USER-BOCS
2018-05-05 10:21:21 -04:00
81293b0fda
changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style
2018-05-05 10:21:11 -04:00
88dca11b3c
update colvars dependencies
2018-05-05 02:36:02 -04:00
460e8bd298
add return value to non-void function
2018-05-05 02:35:42 -04:00
ce86ff6cd1
add missing USER-MOFFF to Makefile and fix typo
2018-05-05 02:15:36 -04:00
36126ccb7d
be more verbose in USER-PHONON install script when KSPACE is not installed
2018-05-05 02:14:17 -04:00
b7210e931c
more cosmetic changes to silence pedantic warnings
2018-05-04 22:34:20 -04:00
53342a5cec
address a few cosmetic issues flagged by -Wpedantic
2018-05-04 22:17:25 -04:00
d53dc541d8
avoiding variable length array in pair style comb3 by declaring MAXLIB const
2018-05-04 21:48:44 -04:00
974ea3420b
replace variable length array in fix drude/transform with new/delete
2018-05-04 21:45:17 -04:00
c83fedf100
replace variable length array in Molecule class with new/delete
2018-05-04 21:41:23 -04:00
7edeccae80
replace variable length arrays in fix filer/corotate by Memory::create() / Memory::destroy()
2018-05-04 21:14:08 -04:00
e242b37619
cast implicit string objects to char * for C++ standard compliance
2018-05-04 21:13:02 -04:00
9a389c946c
replace variable length arrays in fix rx of USER-DPD with new/delete
2018-05-04 19:36:57 -04:00
1b31b4899a
replace variable length arrays in pair style tdpd with new/delete
2018-05-04 19:06:36 -04:00
d24885f805
replace variable length array in fix lb/momentum with fixed size array
2018-05-04 19:00:43 -04:00
345c212828
replace variable length arrays in compute basal/atom with new/delete
2018-05-04 18:55:22 -04:00
477d9feb5c
replace variable length arrays in fix gcmc with new/delete
2018-05-04 18:48:43 -04:00
0a835c499a
fix newly introduced bug
2018-05-04 18:32:41 -04:00
6dcee30b1a
replace variable length arrays in fix gle with new/delete
2018-05-04 18:21:22 -04:00
5670dc5e6e
replace variable length array in msm with new/delete
2018-05-04 18:09:25 -04:00
b11757adb3
replace variable length array in fix ipi with new/delete
2018-05-04 16:47:29 -04:00
b61834f28d
replace variable length array with fixed size
2018-05-04 16:34:46 -04:00
1d54c93df8
replace variable length array with new/delete in PNG support of dump image
2018-05-04 16:30:52 -04:00
330f29db0b
replace variable length arrays in USER-PHONON with new/delete
2018-05-04 16:26:48 -04:00
366aaf2450
port bugfix for single/bond to single/angle and single/dihedral
2018-05-04 00:32:13 -04:00
c9d41178d8
update logfiles and adjust some example inputs to be consistent
2018-05-03 23:37:01 -04:00
6886dcb2e4
correct minor issues, so LAMMPS compiles again
2018-05-03 23:04:07 -04:00
23f71ee4ad
fix bug in create_bonds, where ghost atoms were counted incorrectly
2018-05-03 22:34:11 -04:00
844858d3a7
2nd set of updates
2018-05-03 17:00:08 -06:00
2b8576c7c7
first updates
2018-05-03 16:55:22 -06:00
eeee2d3026
Merge pull request #803 from jrgissing/fix_bond_react
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Fix bond react
2018-05-03 14:16:46 -06:00
53cc609c4c
make filenames comply with LAMMPS conventions and add reference log files
2018-05-03 16:03:37 -04:00
c8a0689d78
correct typo in converting c-library header includes to c++ styles
2018-05-03 15:44:17 -04:00
28786ef99b
tweak to header file names
2018-05-03 11:49:27 -06:00
749f1ff407
Merge pull request #875 from akohlmey/collected-small-fixes
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Collected small changes and bug fixes for the next patch release
2018-05-03 11:28:00 -06:00
654fec164d
Merge pull request #881 from akohlmey/cplus-plus-style-includes
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Replace C-style include files with their C++ equivalents
2018-05-03 11:25:51 -06:00
35294dafbc
Merge pull request #883 from giacomofiorin/colvars-update
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Fixes to Colvars library (version 2018-04-29)
2018-05-03 11:25:32 -06:00
83f5c331cd
Merge pull request #886 from lammps/snap-quadratic
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updates to quadratic form of SNAP potential
2018-05-03 11:21:29 -06:00
1fdb010c41
Revert "workaround for ISFINITE() macro to work with the latest KOKKOS library update"
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This reverts commit f202f1bcf6
2018-05-03 13:08:15 -04:00
b5b70b429f
update log files for SNAP package examples to reflect current state of keywords.
2018-05-03 13:00:24 -04:00
07a15a719f
whitespace cleanup
2018-05-03 12:38:24 -04:00
75cffc78c5
updates to quadratic form of SNAP potential
2018-05-03 10:23:50 -06:00
0c005f5cb0
Small fixes to Colvars library
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Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.
6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
2018-05-02 15:03:56 -04:00
fc0110a2e0
Update fix_bocs.cpp
2018-05-02 13:25:26 -04:00
072a063afc
Delete fix_bocs.html
2018-05-02 11:30:25 -04:00
fbf96b680b
Delete MOD_COMPUTE_H
2018-05-02 11:29:41 -04:00
ed3f8d4b3f
Update methanol.lmp
2018-05-02 11:28:44 -04:00
efbee4a292
Delete man_fix_bocs.html
2018-05-02 11:27:31 -04:00
2e2f19770c
Removed .html files. Removed compute.h mods. Cast pressure for functions
2018-05-02 11:14:30 -04:00
59b59573a7
Added documentation for compute_pair_entropy_atom
2018-05-02 16:10:31 +02:00
25ac1fd16c
mention that fix reax/bonds and reax/c/bonds do not honor the group id
2018-05-01 18:55:00 -04:00
51d2625daf
First fully working version of compute_pair_entropy_atom
2018-04-30 19:40:18 +02:00
4e6188cff6
pair_entropy_atom workin - avg missing
2018-04-28 09:01:09 +02:00
ca6f99129d
revert <cinttypes> back to <inttypes.h> as the former seems to require C++-11
2018-04-27 18:39:11 -04:00
0015b15b18
revert <cstdint> back to <stdint.h> as the former seems to require C++-11
2018-04-27 18:25:30 -04:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
6b92826a1a
Remove Kokkos deprecated code
2018-04-27 12:35:00 -06:00
f202f1bcf6
workaround for ISFINITE() macro to work with the latest KOKKOS library update
2018-04-27 14:15:32 -04:00
d504dcc465
Some changes to compute_pair_entropy_atom
2018-04-27 17:50:35 +02:00
eaaad3f6d5
Commit JT-2 042618
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- commit after after rebase
- some #include were needed
2018-04-26 15:48:34 -06:00
75069ec55b
Commit JT-1 042618
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- new version DMI
2018-04-26 15:26:31 -06:00
392816a807
Commit JT 042418
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- adding the README
- some corrects pair_spin*.cpp/h
2018-04-26 15:26:31 -06:00
1b8669c620
Commit JT 042018, new spin/precession and pair/spin (peru virtual)
2018-04-26 15:26:31 -06:00
ce80d1a3ea
Commit JT 041618
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Enabling multiple exchange interactions
2018-04-26 15:26:31 -06:00
8709f6044b
Commit modifs before release 2 (04/02/18)
2018-04-26 15:26:31 -06:00
a315599bac
Commit modifs before release 1 (03/26/18)
2018-04-26 15:26:31 -06:00
08bc115380
Commit before meeting 032218
2018-04-26 15:26:13 -06:00
65b7e43a91
Examples and docs
2018-04-26 15:25:23 -06:00
436a5de3a6
Documentation V1
2018-04-26 15:25:23 -06:00
f0cca6fb9d
rm pdf equations
2018-04-26 15:21:41 -06:00
3ed640666f
Delete pair_spin_exchange_function.pdf
2018-04-26 15:21:41 -06:00
6a9ecde742
rm one file
2018-04-26 15:21:41 -06:00
2a3b93ca3d
First commits last version doc
2018-04-26 15:21:41 -06:00
e4c6c46b4c
Commit JT 010318 (before APS)
2018-04-26 15:21:41 -06:00
7990826ca2
Commit JT 021518
2018-04-26 15:21:41 -06:00
fa499ff95d
Commit JT 021318
2018-04-26 15:21:41 -06:00
86cfbb3010
Delete in.spin.read_data
2018-04-26 15:15:16 -06:00
f409f4ff53
Commit JT 021318
2018-04-26 15:02:15 -06:00
eab737a45c
Delete Co_PurjaPun_2012.eam.alloy
2018-04-26 15:01:43 -06:00
b422480002
Commit JT 021318
2018-04-26 15:01:43 -06:00
3d18f55155
commit JT 020818
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- adding files for doc and reorg.
2018-04-26 15:01:43 -06:00
10b38cda93
commit JT 020818
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- documentation v1.0
- reorg. of examples
2018-04-26 15:01:43 -06:00
6490ee46b7
Commit JT 020618
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- Documentation
- Memory leaks solved
2018-04-26 14:58:43 -06:00
642c8f9859
Commit JT 020518
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Begin work documentation
2018-04-26 14:58:43 -06:00
755bda2275
Commit JT 020118
2018-04-26 14:58:43 -06:00
05a7e5011f
Commit JT 012318
2018-04-26 14:58:43 -06:00
3abb7f0eaf
Commit JT 011718
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Correction bug in fix/integration/spin
2018-04-26 14:58:43 -06:00
5b93fc6a27
Commit JT 011617
2018-04-26 14:58:43 -06:00
1e096d77ef
Commit JT 011518
2018-04-26 14:58:43 -06:00
38e940a392
beautyfy shell script
2018-04-26 14:58:43 -06:00
7cc62f4234
minor updates on examples/SPIN
2018-04-26 14:58:43 -06:00
01f378d265
minor updates on examples/SPIN
2018-04-26 14:58:43 -06:00
ab200cff06
- linked list in the integration algorithm
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- new version of the coord2sector function
- possible to read_data a spin .data file
2018-04-26 14:58:43 -06:00
5fe0b0a2cc
Delete in.cobalt_dev
2018-04-26 14:58:42 -06:00
6df54ac3ec
Delete in.cobalt_SD
2018-04-26 14:58:42 -06:00
1e9d91bd8f
Delete in.co_magnetomech
2018-04-26 14:58:42 -06:00
749336ae1f
Delete in.kagome
2018-04-26 14:58:42 -06:00
925e647acf
Commit integ
2018-04-26 14:58:42 -06:00
148d26d943
Delete in.cobalt
2018-04-26 14:58:42 -06:00
2bfd30f7d7
Delete in.BFO
2018-04-26 14:58:42 -06:00
f4bb33de4b
Memory corrections
2018-04-26 14:58:42 -06:00
49f0a7a89a
New MPI algorithm (still to be checked)
2018-04-26 14:58:42 -06:00
f1182df776
Commit MPI algorithm
2018-04-26 14:58:42 -06:00
1828274a99
new vmd shell to prepare vmd runs
2018-04-26 14:58:42 -06:00
813343928a
moving files into proper directories
2018-04-26 14:58:42 -06:00
cc44a8863c
Commit 11/06/17
2018-04-26 14:58:42 -06:00
f3e58440a2
Commit 11/6/17
2018-04-26 14:58:42 -06:00
4cbda74df4
Commit new serial algorithms
2018-04-26 14:58:42 -06:00
c6bb9586ef
Commit before new serial algo
2018-04-26 14:58:41 -06:00
b219392d59
Commit before pull on SOLO
2018-04-26 14:58:41 -06:00
f6b4587fe8
Commit Julien 10/24/17
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Correction in the pair/exchange for energy preservation
2018-04-26 14:58:41 -06:00
72d9795d7f
Commit Julien 10/19/2017
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- New files for the pair interactions
- New files for the documentation
- Spin orbit coupling via Neel approach
2018-04-26 14:58:41 -06:00
54832a8fe4
Commit Julien 09/14/17
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- Changes and corrections in the computation of the energy
- Issue with newton_pair in the compute of pair
2018-04-26 14:58:41 -06:00
d144ab0164
Commit Julien 09/06/17
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- units of J1_mag and J1_mech
- correct of pack and unpack in atom_vec_spin
- add conditions in fix_integration_spin
2018-04-26 14:58:41 -06:00
87993368f9
Commit Julien 08/24/17
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- in pair_spin, magneto-mech force for exchange
- compute and added in integration_spin
2018-04-26 14:58:41 -06:00
3de0cf5ab4
Commit Julien 2 08/23/17
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- reorganized includes
- start work on magneto-mechanic potential (adding function)
- renamed fix_nve_spin into fix_integration_spin
2018-04-26 14:58:41 -06:00
f5ff30df83
Changes for coupling magnetomech:
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- hybrid_overlay friend with fix_nve_spin
- modif of the allocation of pair classes in fix_nve_spin
- modif input file for hybrid/overlay eam - spin/pair
- new file for cobalt eam potentials
2018-04-26 14:58:41 -06:00
45ea7b3cc7
First version of the spin tutorial (2)
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Examples (example/SPIN), for BFO and Co
2018-04-26 14:58:41 -06:00
023b018ed2
First version of the tutorial for spin simulations
2018-04-26 14:58:41 -06:00
64b08d3ca8
add write_data() support to remaining improper styles.
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with this commit, write_data() support should be complete.
2018-04-26 16:39:31 -04:00
c7edc6636a
make sure all allocatable class pointers are initialized to NULL
2018-04-26 16:13:19 -04:00
98a22c2b55
Simple test in fix_nve_spin
2018-04-26 13:08:55 -06:00
b88f7aac32
Begining work on test for sectoring (works only if sectoring possible when mpi option is on)
2018-04-26 13:08:55 -06:00
7519dee502
Changes 2 (modif/corrects parallel)
2018-04-26 13:08:55 -06:00
8746ab547e
Small modif and correc of the parallel implemetation
2018-04-26 13:08:54 -06:00
2c5597ae4b
Commit with last changes (sectoring parallel implementation)
2018-04-26 13:08:54 -06:00
8a56b8ad3a
First version of the parallel algorithm
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Performed by sectoring (1, 2, 4, or 8 chuncks) each process.
2018-04-26 13:08:54 -06:00
b934621651
Implementation of SeqNei V1 (Real)
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Still both Seq and SeqNei versions
In SeqNei, loop on Neighb not working yet
2018-04-26 13:08:54 -06:00
bf5b3f96e9
Implemetation of SeqNei Algo 1
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Still Seq and SeqNei versions
Loop on Neigh in SeqNei not working yet
2018-04-26 13:08:54 -06:00
4d375e72f0
Changes: - DMI and ME interactions
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- Computation optimisations
- lot of removed prints
Next work: - Sequential algo implemetation
- temperature simulations (check)
- Work on parallelization
2018-04-26 13:08:54 -06:00
7cc59fbbbe
Same commit, beginning removing prints/checks and pushing
2018-04-26 13:08:54 -06:00
d53def5853
Field compute error apparently corrected. The issue was related to the reverse communication.
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To do:
- Remove all checks/prints used to debug
- Check all the flag set in the atom_vec_spin creator (very important for the reverse comm)
- Code DMI/ME interactions
- Start to work on parallel implementation of the integration
2018-04-26 13:08:54 -06:00
af45d55b3f
Added:
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- For Paramag. simulations, the option "atom_modify" has to be set
ex: atom_modify sort 1000 4.0 (Freq,Dist).
- Actual time is now printed (c_mag[0] in compute_spin)
- Value of Gilbert's damping corrected
- Now even results for SD/Lammps comp. in purely paramg. or aniso. situations
- Pack and unpack reverse needed corrections (f only was set, not fm)
- Spin temperature is now computed (data c_mag[7] in spin_compute)
To do:
- Fcc with p p p bc is still not working
- If Zeeman/Aniso force not defined, error => to be removed
- Add DMI and ME (see if new file or add in the exchange file)
2018-04-26 13:08:54 -06:00
3168704858
For paramagnetic simulation (no pair interaction declared), the "atom_modify" command has to be used (in order to initialize the bin).
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example: atom_modify sort 1000 4.0 (Freq. of sorting, Cutoff distance)
In order to print the actual time with the total mag., the vector associated to the mag. compute was modified. It is now: [time, Mx, My, Mz, |M|, En_mag]
Optimization of the spin_compute routine: energy and mag. have been gathered in a same loop.
2018-04-26 13:08:54 -06:00
bf18d84273
Same commit, with input (mag. cobalt) and vmd files
2018-04-26 13:08:54 -06:00
9b0f8a0c55
First commit for the SPIN package.
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Changes to come:
-Exchange interaction computation to check (loop on neighbors),
-Temperature/random fluctuations to correct (effects too strong),
-Physical results to check,
-Add final interactions (DMI, ME, Dipolar),
-Compute spin temperature (Nurdin and Ma formslisms),
-Work on MPI parallelization,
-Ewald sums to implement (see with Stan's pakage),
-See for prefered magnetic axis (Mitchell's idea),
2018-04-26 13:08:54 -06:00
56d0014a4a
Added #include "citeme.h"
2018-04-26 10:05:49 -04:00
26d22a4b7a
restrain energy must be incremented. bugfix from robert meissner posted to lammps-users
2018-04-26 10:02:42 -04:00
c5e884fb41
USER-BOCS
2018-04-26 09:34:47 -04:00
c4373c7afa
add extract to fix_group
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this will allow users to define groups that are by default created internally by fixes, etc.
2018-04-24 22:53:54 -06:00
69665c218a
Merge pull request #9 from lammps/master
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rebase
2018-04-24 22:09:17 -06:00
6f9a2245d2
add write_data() support to 4 more dihedral styles, which completes the set
2018-04-23 16:56:19 -04:00
d5ec76290b
patch 20Apr18
2018-04-20 17:22:38 -06:00
836027dbd8
Merge pull request #867 from stanmoore1/kk_tweaks
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Tweaks to KOKKOS package
2018-04-20 14:35:58 -06:00
c5127eca89
Merge pull request #872 from akohlmey/ave-correlate-long-bugfix
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Bugfix for fix ave/correlate/long
2018-04-20 09:30:02 -06:00
91b407570a
docfix
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remove mention of as yet unreleased feature
2018-04-19 20:23:58 -06:00
5bf8e1bc5b
add ability to retrieve the number of local rows for computes returning local data
...
this is done supporting the combination of type == 2 with style == 0,
i.e. a local scalar, which is not available in C++ (but there one can
access the compute style data member directly. for the python interface,
the pointer is automatically dereferenced and returned as a c_int.
2018-04-19 18:37:15 -04:00
164537cf37
whitespace cleanup
2018-04-19 18:30:51 -04:00
f1ee46cc64
add check to require atom attribute molecule to avoid segfaults, when it is missing
2018-04-19 18:24:19 -04:00
caa990746e
bugfix
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fixes crash e.g. when building on Ubuntu for Windows
thanks to Márk Jenei (University of Cambridge) for submitting error report
2018-04-18 22:27:12 -06:00
a087813d01
incorporate bugfix for fix ave/correlate/long from jorge ramirez
2018-04-18 07:26:13 -04:00
48e42a4e1e
Merge pull request #824 from jrgissing/write_data-noextra
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Write_data nofix option
2018-04-13 10:27:21 -06:00
6027de5387
Merge pull request #870 from lammps/doc-tweak
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add info to compute heat/flux doc page and a small update to the developer's guide
2018-04-13 10:26:31 -06:00
398f3173aa
remove trailing whitespace
2018-04-13 11:38:02 -04:00
798fcacd77
update example for API change in Fix::copy_arrays()
2018-04-13 11:37:51 -04:00
bc0fd5496a
add info to compute heat/flux doc page
2018-04-13 08:57:24 -06:00
430027465f
Merge pull request #868 from junghans/latte
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cmake: update latte to v1.1.1
2018-04-13 08:44:59 -06:00
7f9400eadc
Merge pull request #865 from athomps/fix_gcmc_temperature
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Made ndof dynamic for temperature fixes and computes
2018-04-13 08:44:41 -06:00
1b965d4d3a
Merge pull request #863 from ellio167/kim-update
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KIM API interface update
2018-04-13 08:43:56 -06:00
6e31b7da63
doc typos
2018-04-11 22:06:22 -06:00
8f1487fbc6
update lib/latte/Install.py to be consistent with CMake config
2018-04-11 11:20:39 -04:00
e2bc4d461e
cmake: update latte to v1.1.1
2018-04-10 17:26:16 -06:00
dee945c01d
cmake: bump openkim to v1.9.4
2018-04-10 15:44:13 -06:00
bc49ce611a
restore python3 compatibility
2018-04-09 23:08:49 -04:00
72cd13aac7
cmake: add openkim build as external project
2018-04-06 17:22:54 -06:00
49d524e442
Remove unused variables in pair_reaxc_kokkos
2018-04-05 11:58:47 -06:00
3c6102a0c3
Tweak whitespace in Makefile.kokkos_cuda_mpi
2018-04-05 11:49:57 -06:00
4517c85c77
Use reference to improve performance in pair_reaxc_kokkos
2018-04-05 11:47:22 -06:00
aa4f044709
Deallocate views of views in serial to prevent race condition in Kokkos profiling tools
2018-04-05 11:44:19 -06:00
2d4e0fcfd3
purge deleted file in KIM package
2018-04-04 13:24:05 -04:00
4fa95de91c
update logfiles for gcmc example inputs
2018-04-04 12:33:48 -04:00
24e0ca5377
avoid warning about group all
2018-04-04 12:28:20 -04:00
e1a17d428f
print the warning about using group all with fix gcmc only from MPI rank 0
2018-04-04 12:26:43 -04:00
8e3ba36a4f
Merge pull request #866 from lammps/header-error-messages
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add placeholders to include files for error messges
2018-04-04 09:45:07 -06:00
12bc84163d
remove or reformulate references to USER-CUDA package, which no longer exists
2018-04-04 11:06:20 -04:00
5221ac2d55
add placeholders to include files for error messges
2018-04-03 17:48:31 -06:00
af8e258ebb
Revert to previous code without plug-in interface
2018-04-03 17:17:23 -05:00
d1356c1d76
Made ndof dynamic for temperature fixes and computes
2018-04-03 15:07:04 -06:00
3f3bab4e71
Create KIM_LAMMPS_PlugIn.h & related changes
2018-04-02 11:45:35 -05:00
f089d8d247
use correct installed kim lib when adding new models
2018-04-02 09:39:44 -05:00
25d2f4b1f6
Update pair_kim for v1.9.4 and versatile linking
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Use dlopen instead of directly linking to kim-api
library. This will allow for easier distribution
of LAMMPS with support for KIM Models.
2018-04-02 09:39:44 -05:00
020fc66ad9
Merge pull request #8 from lammps/master
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rebase
2018-04-01 12:55:58 -06:00
0bfb6f0c2a
Merge branch 'master' of github.com:lammps/lammps
2018-03-30 15:22:15 -06:00
7786cb5a4b
patch 30Mar18
2018-03-30 15:21:55 -06:00
e476f89b47
Merge pull request #860 from lammps/doctweak
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alphabetize correction in docs
2018-03-30 10:10:34 -06:00
bfc07712cf
alphabetize correction in docs
2018-03-30 09:48:15 -06:00
ee5ad9cbb3
Merge pull request #857 from lammps/resetids
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new reset_ids command and dump_modify delay option
2018-03-30 09:45:02 -06:00
a19e8fb269
Merge branch 'master' into resetids
2018-03-30 09:15:24 -06:00
81caeffb38
Merge pull request #855 from lammps/dumpinc
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new dump_modify refresh and compute displace/atom refresh commands fo…
2018-03-30 09:07:19 -06:00
a4795df5f9
complete integration of reset_ids into the documentation build system
2018-03-30 10:49:38 -04:00
ef8423918a
fix typo
2018-03-29 17:04:53 -04:00
0984e94c04
Merge pull request #858 from junghans/fix_return
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MathSpecial::fm_exp: fix return value on ppc64
2018-03-29 08:11:33 -06:00
2a930dac42
Merge pull request #856 from akohlmey/fix_srp_bugfix
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Bugfix for SRP with triclinic cells
2018-03-29 08:10:55 -06:00
09313cf3b5
shift files into doc/src
2018-03-28 13:35:13 -06:00
6dff29bb9c
remove files that were added in error last summer by a pull request
2018-03-28 13:52:07 -04:00
c664f46b31
MathSpecial::fm_exp: fix return value on ppc64
2018-03-28 11:51:04 -06:00
5fd17670b1
new reset_ids command and dump_modify delay option
2018-03-28 11:31:35 -06:00
b37664b44e
squash bug in fix srp that was incorrectly comparing cutoffs for triclinic cells
2018-03-28 10:57:13 -04:00
b5b0f67bcd
Merge pull request #852 from akohlmey/collected-small-bugfixes-and-updates
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Collected small bugfixes and cleanups
2018-03-27 15:43:57 -06:00
a524d8c193
Merge pull request #854 from lammps/readdump
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new option *add keep* added to read_dump
2018-03-27 14:39:35 -06:00
b571f5423a
Merge pull request #850 from lammps/addlib
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a few new lib interface methods
2018-03-27 14:39:16 -06:00
2aef3a0e96
new dump_modify refresh and compute displace/atom refresh commands for incremental dump files
2018-03-27 14:37:04 -06:00
da9f63210e
rephrase error message, remove trailing whitespace
2018-03-27 13:59:21 -04:00
e8b8428f6b
new option *add keep* added to read_dump
2018-03-27 10:08:58 -06:00
1956d93af9
doc tweak on added lib functions
2018-03-27 09:58:53 -06:00
48509622fe
fix bug reported in issue #851
2018-03-26 11:51:00 -04:00
6d0b53ff16
Merge pull request #7 from lammps/master
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rebase
2018-03-24 09:54:32 -06:00
f38169f19c
do not capitalize library.cpp, even if it is at the beginning of a sentence
2018-03-23 16:08:40 -04:00
24e48760da
Merge pull request #845 from akohlmey/dummy-pair-restart-warning
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More consistent and transparent handling for force styles with restarts
2018-03-23 13:47:43 -06:00
b5ee713779
Merge pull request #849 from stanmoore1/kk_deprecated
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Remove deprecated Kokkos code
2018-03-23 13:42:39 -06:00
e73663d1de
Merge pull request #847 from akohlmey/collected-small-changes
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Collected small changes and bugfixes
2018-03-23 13:41:22 -06:00
5770a59ead
Merge pull request #846 from akohlmey/pdf-manual-reorg
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Refactor PDF Manual Structure
2018-03-23 13:40:35 -06:00
db5a6b272b
Merge pull request #842 from martok/meamc-bugfix
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MEAM/C Improvements/fixes
2018-03-23 13:40:14 -06:00
318877ada3
Merge pull request #839 from oywg11/master
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New registry dependent interlayer potential in LAMMPS
2018-03-23 13:38:48 -06:00
d14c16a47c
a few new lib interface methods
2018-03-23 13:34:22 -06:00
5a341bee09
minor cleanup in docs and updated log files for kolmogorov/crespi/full
2018-03-23 06:42:04 -04:00
78e09e1854
refine the code and documentation
2018-03-23 13:26:40 +03:00
c398eb6b57
update kolmogorov-crespi examples
2018-03-22 19:42:07 -04:00
8de7c449fc
refactor code and examples to match LAMMPS conventions. whitespace cleanup. shorten examples.
2018-03-22 19:31:41 -04:00
04c968362f
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
a6d10ba91d
Remove deprecated Kokkos code
2018-03-22 11:19:17 -06:00
b2194d617b
update logs for eff and reax
2018-03-21 21:26:46 -04:00
8bbefb6187
more meaningful output for electron units. fix bug in time unit to fs conversion
2018-03-21 20:12:14 -04:00
07a8e31623
update BOP input and log files
2018-03-21 19:45:52 -04:00
9f785a4f0b
detect and error out on unsupported/old bop potential files
2018-03-21 19:40:25 -04:00
a19f550c1e
update the bop potential file and input
2018-03-21 19:40:03 -04:00
a585871251
update logfiles
2018-03-21 19:04:06 -04:00
ad87b632ef
update spc/e data and reax/c input
2018-03-21 19:03:02 -04:00
192f83164c
Merge branch 'master' of https://www.github.com/lammps/lammps
2018-03-21 17:04:04 -04:00
78d8be311c
Commit before merge.
2018-03-21 17:04:01 -04:00
57dbad59c0
update missing data files and adjust input files for potentials comparison
2018-03-21 16:03:21 -04:00
96061b854b
Merge branch 'compute_chunk_atom_pbc' of https://github.com/poppik/lammps into collected-small-changes
2018-03-21 15:34:05 -04:00
c58bc6fcba
Fixed pbc wrapping in case of spherical bins
2018-03-21 21:20:15 +03:00
e66c71e1ca
fix linker error bug with fftw3 and -DFFT_SINGLE
2018-03-21 12:13:09 -04:00
1a402d4002
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
69ca8e5503
print a message about the restored atom style
2018-03-19 18:57:28 -04:00
5cdc6097f4
abort with an error when a pair style incorrectly advertises a restart ability
2018-03-19 18:25:18 -04:00
28a922b18b
print error message when a pair style was not re-specified after reading a restart
2018-03-19 18:05:47 -04:00
16054cc327
print names of restored force field styles to screen and logfile
2018-03-19 18:04:08 -04:00
3c94f7d5d1
add pointer Force class to temporarily hold the name of the restarted pair style
2018-03-19 18:03:13 -04:00
c2c49395bd
write the name of a pair style to the restart even if it does not store data
2018-03-19 18:00:48 -04:00
f6c76e04b8
patch 16Mar18
2018-03-19 08:26:58 -06:00
545e40f107
MEAM/C: Remove unused function
2018-03-19 13:33:58 +01:00
8e5d3802ad
avoid possible memory leak
2018-03-16 19:11:30 -04:00
3befd4b603
Merge pull request #843 from akohlmey/whitespace-cleanup
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Whitespace cleanup for stable release
2018-03-16 14:44:30 -06:00
e9ac8ba01e
cleanup embedded or trailing tabs
2018-03-16 13:21:54 -04:00
a25e36abea
Avoid more div by zero in meam/c
2018-03-16 17:45:57 +01:00
59dbb49cf9
remove trailing whitespace
2018-03-16 12:37:27 -04:00
ee862d8bf5
replace leading tabs
2018-03-16 12:34:33 -04:00
ac97c2156f
Improve style, replace pow(x) with faster square() and cube()
2018-03-16 16:38:23 +01:00
fc3de22c17
Merge pull request #841 from stanmoore1/compiler_warnings
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Fix compiler warnings
2018-03-16 09:26:59 -06:00
ab914a9220
Merge pull request #840 from akohlmey/collected-small-fixes
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Collected small fixes for stable release
2018-03-16 09:25:59 -06:00
7c300eebd5
Merge pull request #837 from akohlmey/reaxff-bugfix-from-scm
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reaxff corrected bond order bugfix
2018-03-16 09:25:38 -06:00
94a923191a
more whitespace cleanup
2018-03-15 22:02:02 -04:00
7d2ada9d80
whitespace cleanup
2018-03-15 21:57:45 -04:00
15a9600569
Fix compiler warnings
2018-03-14 13:27:03 -06:00
d62534665f
correct potential out-of-bounds memory access
2018-03-14 12:11:58 -04:00
6415befb5b
Add more examples
2018-03-14 16:30:54 +02:00
d00908ea3e
whitespace cleanup
2018-03-13 23:02:55 -04:00
6965307250
print warning when "compress yes" is ignored with delete_atoms
2018-03-13 22:58:39 -04:00
bbb2a6d641
Finally updated the github tutorial
2018-03-13 17:43:25 +02:00
375cf6124f
Finally updated the github tutorial
2018-03-13 17:27:23 +02:00
d9c6278844
Merge pull request #838 from zozo123/replaced-strcmpi-with-strncmpi-to-limit-number-of-chars-compared
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Tools/Matlab: Allow to read LAMMPS output fields
2018-03-12 16:39:35 -06:00
821b18641d
kokkos version of reaxff corrected bond order bugfix from Tomáš Trnka trnka@scm.com posted on lammps-users
2018-03-12 16:58:03 -04:00
ce4ffe5933
Merge pull request #833 from stanmoore1/kk_update_2.6
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Update Kokkos library to v2.6.00
2018-03-12 13:51:33 -06:00
9c3296aad2
Tools/Matlab: Allow to read LAMPPS output field
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Some output fields have attributes attached on the same
line. e.g. "ITEM: BOX BOUNDS pp pp pp". This patch replaced all
the strcmpi to strncmpi in order to limit the number of character
compared with LAMPPS outputs.
Signed-off-by: Yossi Eliaz <eliaz123@gmail.com >
2018-03-12 13:45:13 -05:00
b2c8c40204
reaxff corrected bond order bugfix from Tomáš Trnka trnka@scm.com posted on lammps-users
2018-03-12 12:15:37 -04:00
25c46593ee
protect OpenMP header include with ifdefs
2018-03-12 11:56:54 -04:00
70c5f3bff8
Merge pull request #6 from lammps/master
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rebase
2018-03-11 17:01:20 -06:00
35abbab966
Merge pull request #835 from junghans/fix_python
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lammps.py: inconsistent use of tabs and spaces in indentation
2018-03-09 08:42:15 -07:00
d358e886c5
Merge pull request #834 from akohlmey/new-reax-logs
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provide new reference outputs for various reaxff examples
2018-03-09 08:41:44 -07:00
62d446668c
lammps.py: inconsistent use of tabs and spaces in indentation
2018-03-08 16:23:44 -07:00
fcfbdb13ab
provide new reference outputs for various reaxff examples
2018-03-08 18:10:28 -05:00
39786b1740
Update Kokkos library to r2.6.00
2018-03-08 10:57:08 -07:00
0c4c002f34
patch 8Mar18
2018-03-08 08:19:46 -07:00
bad1cdde78
Merge pull request #831 from lammps/mpi4py-version
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allow for mpi4py version 2 or 3 in Python wrapper
2018-03-07 14:01:22 -07:00
626ca25d05
Merge pull request #830 from akohlmey/more-fixes-for-stable
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More small fixes for stable release
2018-03-07 14:00:32 -07:00
a1bb877d55
correct commented out MPI examples
2018-03-07 11:17:03 -05:00
63c0a35fab
remove code that has no effect
2018-03-07 11:12:08 -05:00
812572ea97
update dependencies for colvars library
2018-03-07 10:57:56 -05:00
f91c36878c
remove dead code
2018-03-07 10:57:07 -05:00
fd1edaf04f
allow for mpi4py version 2 or 3 in Python wrapper
2018-03-07 08:52:46 -07:00
47e2ca6eb2
apply bugfix to reaxff taper function as described in issue #828
2018-03-07 09:52:14 -05:00
8d6fbd9829
Merge pull request #829 from lammps/restartinfo
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add restartinfo=0 to manbody file it was missing from
2018-03-06 15:17:05 -07:00
070e85b44b
add restartinfo=0 to manbody file it was missing from
2018-03-06 12:45:40 -07:00
3e535633e6
Merge pull request #827 from akohlmey/fixes-for-stable
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Fixes for stable release
2018-03-06 12:33:33 -07:00
64779eb576
documentation update for MEAM to clarify the I,J,K indices in the MEAM parameter file
2018-03-06 13:21:34 -05:00
1ca928b331
dead code removal
2018-03-05 20:33:19 -05:00
a1bdea1dd8
avoid division by zero for pair styles meam and meam/c
2018-03-05 14:03:10 -05:00
49aad1d157
rename noextra flag to nofix
2018-03-04 09:56:22 -05:00
04bd268745
rename noextra flag to nofix
2018-03-04 09:55:44 -05:00
959883ad03
rename noextra option to nofix
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since this corresponds to the `fix` option of `read_data`, calling this flag `nofix` seems more consistent and descriptive.
2018-03-04 09:49:50 -05:00
52446eed6d
make fix bond/react example inputs more similar to other input examples in LAMMPS
2018-03-03 19:34:31 -05:00
e8eeb52636
fix memory leaks detected by valgrind
2018-03-03 19:31:53 -05:00
a323147819
noextra option for write_data
2018-03-03 14:28:35 -07:00
89de70ff32
Merge pull request #4 from lammps/master
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rebase
2018-03-03 14:17:56 -07:00
45555b017d
Merge pull request #728 from danicholson/cluster-fragment-aggregate-fixes
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Cluster/fragment/aggregate bugfixes
2018-03-02 15:52:26 -07:00
54f58faab5
Merge pull request #822 from andeplane/gcmc_mpi_error
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Added error if gcmc is used with molecules on more than one processor
2018-03-02 14:41:03 -07:00
22b6764304
Merge pull request #819 from stanmoore1/package_installed
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Add make package-installed command
2018-03-02 14:40:36 -07:00
39a09d3a54
Merge pull request #814 from stanmoore1/kk_snap_workaround
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Workaround issue in pair_snap_kokkos
2018-03-02 14:40:20 -07:00
812a45451a
Merge pull request #816 from giacomofiorin/colvars-update-2018-02-23
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Collected fixes and updates to Colvars library
2018-03-02 13:15:56 -07:00
0666607ceb
Merge pull request #815 from akohlmey/collected-small-fixes
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Collected small cleanups, fixes, and enhancements
2018-03-02 13:15:35 -07:00
d18ba3b188
Added error if gcmc is used with molecules on more than one processor
2018-03-02 11:23:34 -08:00
b1d3b56a17
apply bugfix reported in issue #820
2018-03-02 04:33:13 -05:00
21364f38b0
gatherv fix, take 2
2018-03-01 23:11:46 -07:00
8d0fdb17a6
Add make package-installed command
2018-03-01 10:39:06 -07:00
eadac15466
avoid multiple calls to delete [] on the same pointer.
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thanks to @ExHP for pointing out this issue
2018-02-28 14:02:16 +01:00
51b19dfd1a
plug memory leak in fix bond/react
2018-02-25 14:10:28 +01:00
58e01a9eee
plug memory leak in pair style lj/class2/coul/long with coulomb tables
2018-02-25 14:03:07 +01:00
3b90f60064
Merge pull request #3 from lammps/master
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rebase
2018-02-24 23:49:27 -07:00
7d1de34533
gatherv fix, doc updates
2018-02-24 22:49:28 -07:00
5fb2979da7
allow dynamic groups for some standard walls interacting with point particles
2018-02-24 13:50:42 -05:00
948f4783aa
ring communication *is* called with outbut set to NULL, so don't error out on that.
2018-02-24 17:17:45 +01:00
fb6e7e8aea
add sanity checks for ring communication
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we do not call memcpy() unless nbytes != 0 and source/target pointer is not NULL
we error out on illegal combinations of nbytes and inbuf/outbuf
2018-02-24 16:41:10 +01:00
bba4bd1489
support offsets for molecule IDs (if available) in read_data similar to atomIDs
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suggested by felipe perez in https://sourceforge.net/p/lammps/mailman/message/36236631/
2018-02-23 18:02:05 -05:00
4a875dc67d
Workaround for compiler bug in gcc v4.9.3, manifest in KOKKOS SNAP
2018-02-23 09:01:34 -07:00
f3cf407a21
Collected fixes and updates to Colvars library
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This commit includes several fixes to moving restraints; also added is support
for runtime integration of 2D and 3D PMFs from ABF.
Mostly changes to existing member functions, with few additions in classes not
directly accessible by LAMMPS. Also removed are calls to std::pow(), replaced
by a copy of MathSpecial::powint().
Relevant commits in Colvars repository:
7307b5c 2017-12-14 Doc improvements [Giacomo Fiorin]
7f86f37 2017-12-14 Allow K-changing restraints computing accumulated work; fix staged-k TI estimator [Giacomo Fiorin]
7c1c175 2017-12-14 Fix 1D ABF trying to do pABF [Jérôme Hénin]
b94aa7e 2017-11-16 Unify PMF output for 1D, 2D and 3D in ABF [Jérôme Hénin]
771a88f 2017-11-15 Poisson integration for all BC in 2d and 3d [Jérôme Hénin]
6af4d60 2017-12-01 Print message when issuing cv delete in VMD [Giacomo Fiorin]
4413972 2017-11-30 Check for homogeneous colvar to set it periodic [Jérôme Hénin]
95fe4b2 2017-11-06 Allow abf_integrate to start in bin with 1 sample [Jérôme Hénin]
06eea27 2017-10-23 Shorten a few constructs by using the power function [Giacomo Fiorin]
3165dfb 2017-10-20 Move includes of colvarproxy.h from headers to files [Giacomo Fiorin]
32a867b 2017-10-20 Add optimized powint function from LAMMPS headers [Giacomo Fiorin]
3ad070a 2017-10-20 Remove some unused includes, isolate calls to std::pow() [Giacomo Fiorin]
0aaf540 2017-10-20 Replace all calls to std::pow() where the exponent is not an integer [Giacomo Fiorin]
2018-02-23 08:34:53 -05:00
0003bb6766
merge capture regions, so the library interface code can compiled with exceptions
2018-02-23 14:20:39 +01:00
523978b4c7
dead code and uninitialized variables detected by clang
2018-02-23 12:04:15 +01:00
d5e43a9ab1
whitespace cleanup and reindent
2018-02-23 10:20:29 +01:00
939b1b2d05
Workaround issue in pair_snap_kokkos_impl
2018-02-22 14:27:23 -07:00
77efd3dfb3
Merge pull request #813 from akohlmey/correct-neighbor-build
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Make default argument for virtual method Neighbor::build() explicit
2018-02-22 08:48:06 -07:00
feb9f29fad
Merge pull request #812 from akohlmey/correct-integrate-setup
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Make default argument for pure method Integrate::setup() explicit
2018-02-22 08:47:45 -07:00
bfdf464ee3
patch 22Feb18
2018-02-22 08:46:03 -07:00
99d5957a01
make default argument of virtual function Neighbor::build() explicit
2018-02-22 08:42:36 -05:00
65acd233ce
forgot to remove one default argument on a method derived from Integrate::setup()
2018-02-22 08:13:54 -05:00
cf3887c5e0
default arguments on polymorph/pure methods can lead to unexpected overloading in derived classes
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argument for Integrate::setup() made explicit
2018-02-22 07:53:58 -05:00
3787b89447
re-add compressed data file (was hidden by .gitignore)
2018-02-22 02:31:25 -05:00
8fef7880e7
dead code removal and loop construct fixes to silence compiler warnings.
2018-02-22 02:23:57 -05:00
a8eb3ff77f
consolidate per-atom property fixes into one
2018-02-21 23:20:17 -07:00
e1d1c87656
Merge pull request #811 from akohlmey/check-latte-version
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Tiny update to fix latte for checking library version
2018-02-21 10:54:58 -07:00
bcef43c7d1
add code to check the ABI version of the LATTE library
2018-02-21 12:11:02 -05:00
aa1503b7e0
Merge pull request #800 from athomps/fix_gcmc_segfault_fix
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Added warning to discourage use of group all and fixed some segfault …
2018-02-21 09:50:22 -07:00
d9d072df65
Merge pull request #809 from Jc11235/fix_neb_old_tangent_implementation
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added old tangent to fix_neb for AGNI potential
2018-02-21 09:49:39 -07:00
a3cd600052
Merge pull request #786 from jrgissing/per_atom_prop_group
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per-atom property dynamic group
2018-02-21 09:48:49 -07:00
53fb7f4015
Merge pull request #810 from lammps/latte-error2
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2nd try on LATTE error returns, plus a couple minor doc edits
2018-02-21 09:47:17 -07:00
38ce56f252
fix documentation issues: non-ASCII characters, broken/missing links, formatting
2018-02-21 11:53:18 +01:00
5191071581
no need to cast fixes to specific styles/types
2018-02-21 11:15:44 +01:00
b6821ed942
since the code uses static ids, only one instance is allowed at a time
2018-02-21 11:15:09 +01:00
deeba53a24
consolidate inclusion file style with LAMMPS conventions
2018-02-21 11:14:32 +01:00
daae906162
move fix bond/react examples and compress large data file
2018-02-21 10:30:35 +01:00
b252866393
sync fix temp/rescale to upstream
2018-02-21 10:17:00 +01:00
a672874186
Update comment
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Clarify the comment as to why this else branch was added and what this represents.
2018-02-21 10:04:13 +01:00
911529ab24
correct typo
2018-02-21 08:43:33 +01:00
a5a47899a3
make XDR support for dump style xtc compile on MacOSX
2018-02-20 22:10:21 +01:00
c399b75dec
2nd try on LATTE error returns, plus a couple minor doc edits
2018-02-20 12:52:12 -07:00
9cf99ef479
Merge pull request #806 from vishalkenchan/new_pair_lj_cut_coul_wolf
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Lennard-Jones with Coulomb interactions accounted through Wolf sum
2018-02-20 11:55:37 -07:00
54740a0668
Merge pull request #804 from akohlmey/collected-small-changes
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Collected small changes for next patch release
2018-02-20 11:54:24 -07:00
9f7b837f34
replace non-ASCII character
2018-02-20 17:18:56 +01:00
a8a38216ae
added old tangent to fix_neb for AGNI potential
2018-02-20 10:06:24 -05:00
54dc73c771
correctly compute adjusted box lengths for triclinic boxes. code taken from topotools
2018-02-19 14:06:26 +01:00
7bd089aa6d
fix typo
2018-02-19 14:05:50 +01:00
d52c5435a7
ignore installed copy of fix bond/react
2018-02-18 17:12:03 +01:00
75a432833b
remove messy hack
2018-02-18 17:11:06 +01:00
5843be1557
move fix bond/react to USER-MISC package
2018-02-18 17:03:40 +01:00
7ec4a5818d
add USER-OMP versions of lj/cut/coul/wolf
2018-02-18 16:38:50 +01:00
44285f818f
more cleanup and respa code removal
2018-02-18 16:37:41 +01:00
98bcf51a45
there is no support for multi-cutoff r-RESPA in lj/cut/coul/wolf
2018-02-18 16:07:00 +01:00
65870843a5
fix typo in stride2() description in variable command docs reported by Jerome Guterl
2018-02-18 15:37:35 +01:00
c864e55adb
Lennard-Jones potential with Coulomb interactions accounted through Wolf summations
2018-02-18 14:20:59 +01:00
c4ea2f2b34
update long-range coulomb message formatting, so it fits better into other kspace output
2018-02-16 14:24:33 +01:00
a641e40e79
use Error::message() instead of Error::warning() to report whether coulomb tables are used or not
2018-02-16 14:11:58 +01:00
3d12cff8a5
Merge branch 'patch-1' of https://github.com/evoyiatzis/lammps into collected-small-changes
2018-02-16 10:55:25 +01:00
b220b647d4
Update error.cpp
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When compiling with g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) an error occurs:
error.cpp: In member function ‘void Error::generate_error(unsigned int, std::string, std::string)’:
error.cpp:146: error: ‘exit’ was not declared in this scope
The fix is to include the #include <cstdlib> where the exit() function is decleared in the error.cpp file
2018-02-16 10:49:08 +01:00
a30ede80a6
avoid triggering misformatting of manual overview table with txt2html
2018-02-15 12:12:19 +01:00
2c4287630d
allow dynamics groups for fix nve/limit and fix temp/rescale
2018-02-15 05:17:15 -05:00
f8daea5f3e
make dihedrals and impropers header output consistent with bonds and angles
2018-02-15 05:13:59 -05:00
2aa693c46c
update authors list and packages from http://lammps.sandia.gov/authors.html
2018-02-15 05:06:54 -05:00
4210abfc79
bugifx for using compute chunk/atom with compress via rerun or right at the beginning of a run
2018-02-13 18:15:17 +01:00
69f813b22e
fix up formatting of tutorials for PDF manual
2018-02-13 16:41:23 +01:00
b3693f891b
different style of AtC page headers that works well with html and pdf
2018-02-13 16:40:50 +01:00
1a213363f1
add group style to create an empty group directly
2018-02-13 14:54:30 +01:00
63714c7079
remove PDF-only .txt file from Sphinx documentation processing
2018-02-13 13:10:20 +01:00
60f411d655
update manual content list for recent updates
2018-02-13 12:47:36 +01:00
7b551bb594
add a short command overview page for the PDF manual only
2018-02-13 12:47:05 +01:00
b0d8fb2170
promote header levels for better formatting in pdf manual
2018-02-13 12:43:56 +01:00
44faa8e9f5
insert new toplevel text into USER-ATC docs, change header levels.
2018-02-13 12:43:32 +01:00
3ceec36b84
improve format
2018-02-13 12:38:48 +01:00
f890cdfb9e
correct formatting in fix atc docs
2018-02-13 11:44:07 +01:00
3a909e15ae
remove non-functional doxygen generated navigation header from AtC doc files
2018-02-13 11:43:52 +01:00
fcf552ffe1
Merge branch 'patch-4' of https://github.com/abbatux/lammps into collected-small-changes
2018-02-13 09:51:02 +01:00
378c5071bf
protect library interface from issuing lammps commands during run and minimize
2018-02-12 14:26:05 -05:00
776f588746
add support for UFM pair style support to OpenCL compilation makefile
2018-02-12 18:43:30 +01:00
a04a975d3a
add large nylon example for parallel validation, reformat doc page
2018-02-11 17:35:47 -07:00
b9eaf98702
avoid uninitialized memory access errors reports from valgrind with fix qeq
2018-02-11 17:09:06 +01:00
afd39eb9b8
correctly represent, that the molecule summary refers to the largest type number and not the number of types
2018-02-11 16:17:24 +01:00
6efeab0f3a
avoid segfault when using a hash as map on an empty system
2018-02-10 20:40:02 +01:00
7e78738c73
patch 5Feb18
2018-02-09 14:26:21 -07:00
8a39ae8585
remove dead code
2018-02-09 17:32:42 +01:00
a6eb521468
strip off unwanted ^M characters
2018-02-09 17:32:32 +01:00
3528f9ca27
fix bugs in documentation and implementation of atom style mdpd
2018-02-09 15:19:01 +01:00
2e99e54e23
Merge branch 'patch-2' of https://github.com/amilumas/lammps into collected-small-changes
2018-02-09 14:44:11 +01:00
a0de2f27a5
avoid segfaults in USER-MESO by checking for required atom style flags
2018-02-08 19:15:09 +01:00
21fe88ffa8
remove dead code in various neighbor list related source files
2018-02-08 13:07:56 -05:00
996c62f4e0
fix bond/react: generalized classical chemical reactions
2018-02-07 21:58:05 -07:00
3d63c29abd
Merge pull request #2 from lammps/master
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rebase
2018-02-07 21:35:26 -07:00
b49806d36a
correct the logic for checking if fix is right
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previously had incorrect logic for checking if fix is acceptable
2018-02-07 16:35:49 -05:00
49745968f2
make link unambiguous so sphinx is not confused
2018-02-06 16:57:27 +01:00
f914da62e0
fix typo
2018-02-06 16:57:27 +01:00
669ae02a85
apply pattern to ignore OPT package sources
2018-02-06 16:57:27 +01:00
1d403b2aa3
Added warning to discourage use of group all and fixed some segfault cases
2018-02-05 13:29:14 -07:00
fa4c7fc664
Merge pull request #781 from wmbrownIntel/user-intel-2018u1p2
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USER-INTEL: Adding missing backslash for two Makefiles using Intel co…
2018-02-02 14:51:23 -07:00
401bfc52e1
Merge pull request #798 from akohlmey/always-use-internal-xdr
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Replace OS provided XDR support with bundled code
2018-02-02 14:47:40 -07:00
984fda5e78
Merge pull request #797 from akohlmey/multifile-restart-bugfix
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Address bug in multifile restart writing with step number included
2018-02-02 14:47:09 -07:00
196b3c81ef
Merge pull request #796 from akohlmey/create-bonds-sanity-check
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Sanity check on created/read-in bonds/angles/dihedrals/impropers
2018-02-02 14:46:46 -07:00
f4a79b4d8e
Merge pull request #794 from akohlmey/tersoff-fixes
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Consistent checking of Tersoff potential parameters
2018-02-02 14:46:11 -07:00
7441b062e9
Merge pull request #792 from pastewka/18_dump_nc1
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Dumping to multiple files failed with an error message complaining about a missing 'append yes' option.
2018-02-02 14:45:52 -07:00
10d80ba9c3
Merge pull request #791 from akohlmey/charmm-cmap-docs-reference
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Update CMAP related docs and rebuild example input decks
2018-02-02 14:44:58 -07:00
5383035828
Merge pull request #787 from akohlmey/user-atc-dep
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Make the USER-ATC package depend on MANYBODY
2018-02-02 14:44:36 -07:00
dc4dd1591f
Merge pull request #785 from jrgissing/imp_dihed_print
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modifications to correctly print modified dihedrals, impropers
2018-02-02 14:44:15 -07:00
e4a1826dee
Merge pull request #783 from numericalfreedom/lammps-doxygen
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Added double quotes to a word in Section_tools.txt file
2018-02-02 14:41:56 -07:00
160edc9532
Merge pull request #782 from hheenen/user-mofff-contribution
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User mofff contribution
2018-02-02 14:41:28 -07:00
553b3ff69a
Merge pull request #778 from athomps/fix_gcmc_segfault_fix
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Fixed recent segfault in fix gcmc and added mcmoves keyword
2018-02-02 14:40:14 -07:00
2913d3da60
Merge pull request #777 from lammps/fix_prop_atom
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Fix bug in FixPropertyAtom
2018-02-02 14:39:42 -07:00
4af14becb5
Merge pull request #710 from rpleite/add-pair-ufm
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Add the UFM pair potential - (GPU/OPT/OMP)
2018-02-02 14:38:28 -07:00
85fdf9eaba
make links to papers unique across files
2018-02-02 10:10:27 +01:00
2ff278defa
fully integrate ufm into documentation
2018-02-02 10:02:44 +01:00
bfcb71a8be
add package file to .gitignore
2018-02-02 09:27:09 +01:00
c3d1cee5f9
try to use OS-provided (and obsoleted) RPC headers for XDR. always use bundled code
2018-02-02 09:23:02 +01:00
3e0cb9b463
rename examples to match usual naming conventions and add reference output.
2018-02-01 18:56:10 +01:00
b70149e86a
include added docpages in toctrees for sphinx
2018-02-01 18:50:25 +01:00
080ce422ae
correct incorrect reference
2018-02-01 18:40:28 +01:00
cc54848f7b
adapt to current manual conventions
2018-02-01 18:40:17 +01:00
090ce7cecb
remove tab char
2018-02-01 18:19:37 +01:00
3bc1c6b59e
Address bug in multifile restart writing with step number included
2018-02-01 14:25:55 +01:00
38715d7f85
do not allow illegal combination of atom IDs in data files for bonds/angles/dihedrals/impropers
2018-01-31 06:08:04 -05:00
54a3096278
do not allow single bond/angle/dihedral definitions with illegal atom ID combinations
2018-01-31 05:59:19 -05:00
17d98d0915
make checking for tersoff parameters consistent across all implementations
2018-01-30 04:53:57 -05:00
9cf4ac8b7c
DOC: Added netcdf and netcdf/mpiio to dump style supporting atom attributes.
2018-01-28 14:24:28 +01:00
4e4fd5f07c
BUG: Dumping to multiple files failed with an error message complaining about a missing 'append yes' option.
2018-01-28 14:23:05 +01:00
9fd1e47968
ignore generated/copied files
2018-01-28 06:24:03 -05:00
6753977837
recreate 1ac7 input deck with up to date tools and LAMMPS binary.
2018-01-28 06:23:09 -05:00
031812b2bf
recreate 1gb1 input deck with CMAP included.
2018-01-28 06:22:03 -05:00
cf8dae5ef3
explain position of fix cmap command in input for data and restart files
2018-01-28 06:20:03 -05:00
ba68548e38
clarify ch2lmp commands purpose in tools section
2018-01-28 06:19:33 -05:00
448c9c8d8a
add a dependency on PairEAM/MANYBODY for installing USER-ATC
2018-01-23 16:27:06 +01:00
13c08225ed
per-atom property dynamic group
2018-01-23 00:16:51 -07:00
d2da49cdf9
modifications to correctly print modified dihedrals, impropers
2018-01-22 23:56:11 -07:00
e72faf3d7f
Added double quotes to a word in Section_tools.txt file in order to activate
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Sphinx hyperlink.
2018-01-21 20:55:04 +01:00
3f967e3d84
cmake: add USER-MOFFF
2018-01-21 08:10:38 -07:00
5212e95787
added src/USER-MOFFF/README
2018-01-21 13:34:02 +01:00
f7e2bf239f
Added MOF-FF src, doc and example files
2018-01-21 11:40:48 +01:00
a802b750a6
USER-INTEL: Adding missing backslash for two Makefiles using Intel compiler.
2018-01-17 21:59:37 -08:00
9bb7f1ddf6
Fixed recent segfault in fix gcmc and added mcmoves keyword
2018-01-17 13:45:15 -07:00
5e9d257ec2
patch 17Jan18
2018-01-17 13:00:48 -07:00
415a55bc3e
Fix bug in fix_property_atom
2018-01-17 10:41:56 -07:00
e1e6825eb2
Merge pull request #776 from numericalfreedom/lammps-tools-doxygen
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Small character corrections to the file Developer.dox.lammps
2018-01-17 07:34:18 -07:00
88a2f9fcc6
Merge pull request #775 from wmbrownIntel/user-intel-2018u1
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USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2…
2018-01-17 07:34:08 -07:00
480d7dd6ce
Merge pull request #774 from lammps/neigh-tweak
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small changes to recent PR to standardize with other npair styles
2018-01-17 07:33:46 -07:00
9b12984378
Small correction in image caption in Developer.dox.lammps
2018-01-17 14:46:44 +01:00
8d29f64236
Small character corrections to the file Developer.dox.lammps
2018-01-17 14:05:30 +01:00
1b91c0eab0
fix typo in docs resulting in broken link
2018-01-16 21:01:25 -05:00
0c8af0704e
Tweak to npair_halffull_newtoff.cpp
2018-01-16 16:43:25 -07:00
f1901237be
small changes to recent PR to standardize with other npair styles
2018-01-16 15:49:16 -07:00
0cd864134d
Merge pull request #765 from stanmoore1/halffull_ghost
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Add ghost option to npair_halffull
2018-01-16 15:39:07 -07:00
bf48f3e240
Merge pull request #758 from mkanski/ci-ReaxFF
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Modification of ReaxFF
2018-01-16 13:04:20 -07:00
23dda3d51b
Merge pull request #770 from numericalfreedom/lammps-tools-doxygen
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Tools for LAMMPS documentation for developers with the "doxygen" documentation platform
2018-01-16 13:02:10 -07:00
5d254855eb
Merge pull request #772 from akohlmey/improved-variable-error-reporting
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More improved variable error reporting
2018-01-16 13:00:42 -07:00
9a70f2d182
Merge pull request #773 from lammps/couple-simple
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update of COUPLE/simple examples
2018-01-16 12:59:51 -07:00
b95cf658c7
remove faulty line of code, left in by accident
2018-01-16 14:10:46 -05:00
709ce8a230
Merge branch 'neigh-identical-check' into couple-simple
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# Conflicts:
# src/create_bonds.cpp
# src/delete_atoms.cpp
2018-01-16 14:09:21 -05:00
2ad823ffd4
correct check for identical requests
2018-01-16 14:08:18 -05:00
4c0cd5f1ad
add short bond cutoff warning also to USER-OMP
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This implements the warning about a total cutoff shorter than 2x bond cutoff also to the USER-OMP variant of reax/c
2018-01-16 13:50:49 -05:00
8d37c89cb6
different bug fix for create_bonds, delete_atoms neigh list issue
2018-01-16 11:32:37 -07:00
21ff4407ab
update of COUPLE/simple examples
2018-01-16 10:48:38 -07:00
f2c0c4a7d1
Merge branch 'lammps-tools-doxygen' of https://github.com/numericalfreedom/lammps into lammps-tools-doxygen
2018-01-16 18:39:08 +01:00
1640066132
Merge remote-tracking branch 'lammps-origin/master' into lammps-tools-doxygen
2018-01-16 18:38:12 +01:00
3b1ec14a68
add a warning if the bonded cutoff is large
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This should print a warning when 2x the bonded interaction cutoff list larger then other cutoffs, as was the setting before the performance optimization with the change in 2690075405
2018-01-16 12:01:47 -05:00
01cfb710ff
propagate printing variable name with error deeper into the code
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this now covers a large set of cases where the variable name can be printed.
it also is complete for the current code, since no more default arguments are required
2018-01-16 11:31:20 -05:00
3de39c70c1
print variable name with errors only for known variables.
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this makes errors for "anonymous" evaluations (if statement, immediate variables) less confusing.
2018-01-16 11:29:48 -05:00
86ed55599d
The bash shell script doxygen.sh has been revised.
2018-01-16 17:28:58 +01:00
e798cdf31f
Merge pull request #771 from stanmoore1/reax_example
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Add ReaxFF Example
2018-01-16 09:05:36 -07:00
97dd812647
Merge pull request #769 from rbberger/cmake_compilation_fixes
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CMake compilation fixes
2018-01-16 09:04:04 -07:00
e07a6d1e34
Merge pull request #768 from akohlmey/collected-doc-fixes
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collected documentation fixes
2018-01-16 09:03:45 -07:00
6e37272c9d
Merge pull request #764 from akohlmey/improved-variable-error-reporting
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Improved error messages when defining or evaluating variables
2018-01-16 09:02:20 -07:00
6bd6e62767
Merge pull request #763 from stanmoore1/kk_neighlist
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Enhance Kokkos Neighbor lists
2018-01-16 09:01:15 -07:00
57dd6c78c1
Merge pull request #761 from stanmoore1/kk_snap
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Kokkos version of Pair SNAP and ZBL
2018-01-16 09:00:52 -07:00
9e413bf57a
Merge pull request #760 from akohlmey/info-coeffs
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New "coeffs" keyword added to "info" command
2018-01-16 09:00:34 -07:00
b374813104
Add reax example
2018-01-16 08:50:30 -07:00
07ddb5e62c
USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2018u1 compilers.
2018-01-15 23:54:48 -08:00
72b479d42e
Add missing return value in pair_snap_kokkos
2018-01-15 11:01:07 -07:00
c8b5d83cc7
mention tool/doxygen folder in tools section and refer to README file
2018-01-15 10:43:30 -05:00
a5998179bf
Fix issues with Kokkos skip lists
2018-01-15 08:23:39 -07:00
26d6f6d1f1
Tools for LAMMPS documentation with the "doxygen" documentation platform
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are provided.
New directory: tools/doxygen
New file: tools/doxygen/Developer.dox.lammps
New file: tools/doxygen/Doxyfile.lammps
New file: tools/doxygen/doxygen.sh
New file: tools/doxygen/README
The Developer.dox.lammps file contains a slightly revised version of the
Developer.pdf file adopted to the LAMMPS "doxygen" documentation.
The Doxyfile.lammps file is a first proposal for a LAMMPS "doxygen"
documentation flavor and can be adjusted to specific requirements.
The "doxygen.sh" shell script generates the LAMMPS "doxygen"
documentation.
Detailed instructions can be found in the README file.
2018-01-15 15:42:31 +01:00
f37f4f0041
support more cases where the variable name is reported on errors
2018-01-14 17:56:03 -05:00
d2983caad4
CMake: limit visibility of COLVARS lepton library headers
2018-01-14 18:01:19 +01:00
2b7c233791
Simplify change to CMake build for USER-COLVARS
2018-01-14 08:44:50 +01:00
9e35e76b8c
Fix issues in Kokkos npair_halffull and npair_skip
2018-01-13 21:32:59 -07:00
7a78875911
Fix issues in Kokkos pair snap and zbl
2018-01-13 21:31:11 -07:00
1cfc3118cc
CMake: remove BUILD_SHARED_LIBS requirement from PYTHON package
2018-01-13 22:17:23 +01:00
23e8fb0542
Update CMake build for USER-COLVARS
2018-01-13 21:57:24 +01:00
72eb2dab52
Add missing math.h header
2018-01-13 20:41:05 +01:00
f6075c9d2c
One last tweak to npair_halffull_newtoff.cpp
2018-01-12 16:12:57 -07:00
24f1889b02
Only include ghosts for newton off, since this style exists as a standalone build, but the newton on method doesn't
2018-01-12 16:10:42 -07:00
dea8d592da
Optimize npair_halffull styles; the number of i atoms, whether owned or ghost, must match between the child half list and parent full list
2018-01-12 15:51:54 -07:00
52d3e98f3b
Fix issue in npair_skip_kokkos
2018-01-12 15:45:24 -07:00
6e3acce3be
Relax restriction in neighbor.cpp
2018-01-12 15:44:11 -07:00
1ec54827d6
Add Kokkos halffull neighbor list capability
2018-01-12 15:41:59 -07:00
61ebf6265a
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
190cc78034
add dummy doc files for not-yet-implemented features
2018-01-12 12:29:03 -05:00
5863f115dd
correctly escape 'a_ ' text, which is not a reference unlike 'a_b '
2018-01-12 12:26:50 -05:00
75d259f5ee
improve PDF reader compatibility for the created PDF file.
2018-01-12 12:00:53 -05:00
3b1b9a2cbf
replace non-ASCII quotation marks with ASCII equivalent
2018-01-12 11:30:27 -05:00
17b6a4c3cd
Added more permanent citation
2018-01-12 11:47:35 +01:00
1c10c78684
Add ghost option to npair_halffull
2018-01-11 15:15:04 -07:00
26917280be
state name of the affected variable in error messages where possible
2018-01-11 15:01:08 -05:00
45674e6cd3
Add Kokkos skip list capability
2018-01-11 10:07:44 -07:00
22d2d1cdf3
Fix issue in pair_snap_kokkos memory_usage
2018-01-11 10:01:34 -07:00
0d7bee40ae
Add newline at end of pair_snap_kokkos_impl.h
2018-01-11 09:41:37 -07:00
db1ed32a51
Fix minor issues in pair_snap_kokkos
2018-01-11 09:39:53 -07:00
d7d087ae67
Fix issue with peratom energy/virial in pair_snap_kokkos
2018-01-10 10:20:40 -07:00
92e2df74c1
Fix bug in Kokkos peratom energy/virial with newton on
2018-01-10 10:20:12 -07:00
92742c5373
Introduced the change in reax/c/omp
2018-01-10 18:00:22 +01:00
2047ae76e3
Move compute_bi outside of j-loop
2018-01-09 17:05:57 -07:00
4adbb882b3
Temper SNAP output
2018-01-09 17:05:34 -07:00
275c08453f
Add Kokkos versions of pair_style snap and zbl
2018-01-09 17:03:49 -07:00
91107cc1f3
add a "coeffs" keyword to the info command for debugging "All XXX coeffs are not set" errors.
2018-01-09 12:47:33 -05:00
e26c170679
Added example and tabulated close-range correction
2018-01-09 15:08:08 +01:00
1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates
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Collected bugfixes and updates for the next patch release
2018-01-08 09:20:18 -07:00
9e9cfe5869
Merge pull request #754 from rbberger/cmake_kokkos_bugfix
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CMake bugfixes for KOKKOS builds
2018-01-08 09:16:43 -07:00
85ff0c1e46
Merge pull request #750 from stanmoore1/kk_fences
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Add Kokkos thread fences to comm pack/unpack routines
2018-01-08 09:16:16 -07:00
cc9b6118b8
Merge pull request #748 from stanmoore1/kk_docs
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Update Kokkos docs
2018-01-08 09:15:36 -07:00
09bed0c09a
Merge pull request #747 from stanmoore1/kk_reax_hist
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Fix broken charge history in fix qeq/reax/kk
2018-01-08 09:15:21 -07:00
1b51efd6b8
Merge pull request #744 from akohlmey/doc-update
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Documentation build updates
2018-01-08 09:15:02 -07:00
8888b05b18
Merge pull request #742 from rbberger/fix_python_move
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Fix python/move
2018-01-08 09:14:36 -07:00
3bb8294f31
Merge pull request #718 from timattox/USER-DPD_es_RNG
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USER-DPD: External State RNG
2018-01-08 09:13:11 -07:00
450c689ae9
Merge pull request #725 from stanmoore1/kk_update
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Update the Kokkos library in LAMMPS to v2.5.00
2018-01-08 09:12:51 -07:00
a5d401e164
Fixed header for the force field file
2018-01-08 14:46:32 +01:00
b96100c0b7
Fixed header for the force field file
2018-01-08 14:42:43 +01:00
2690075405
Performance increase for charge-implicit ReaxFF/changed cutoff selection
2018-01-08 14:38:24 +01:00
f77483e437
adapt #include statements to current LAMMPS conventions
2018-01-06 19:44:07 -05:00
11cddd8798
explicitly include math.h
2018-01-06 19:42:40 -05:00
09ca7b32fc
Revert "no need to include library.o in the LAMMPS executable"
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This reverts commit 4a3a6b4455
2018-01-06 19:47:33 +01:00
3af389e6cf
Revert "no need to include library.o in the LAMMPS executable"
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This reverts commit 4a3a6b4455
2018-01-06 12:58:17 -05:00
46217db8a5
make python functions examples more complete by adding exception handling and initializing variables
2018-01-06 12:56:42 -05:00
d6d7dde653
Add error output if python evaluation failed
2018-01-06 18:54:55 +01:00
6070182f06
correctly account for individually added bonds, angles, and dihedrals
2018-01-06 11:03:48 -05:00
6c058fb56c
avoid division by zero in ewald for empty and uncharged systems. require kspace_modify gewald
2018-01-05 20:14:25 -05:00
91993b236d
avoid division by zero in PPPM for empty and uncharged systems. require kspace_modify gewald
2018-01-05 19:52:51 -05:00
5ecc3ce366
avoid division by zero when trying to run PPPM on a system without atoms
2018-01-04 20:44:40 -05:00
75f1a4f3f0
use filelink.o consistently, since filelink does not work with some compilers, e.g. nvcc
2018-01-04 20:43:53 -05:00
ffc74fca6c
Merge branch 'fix_property_atom_doc_update' of https://github.com/Pakketeretet2/lammps into collected-bugfixes-and-updates
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this closes PR #755
2018-01-04 19:46:31 -05:00
2896df2140
avoid that occasional neighbor lists requested from commands linger around for too long and thus cause segementation faults
2018-01-04 17:16:31 -05:00
c333401e72
Use bold font instead of underscores for emphasis.
2017-12-25 13:27:14 +01:00
a9e9a2046b
Fixes/clarifies the fix_property_atom docs.
2017-12-25 13:03:18 +01:00
d4f45f4f85
correct set command example in fix property/atom
2017-12-24 17:45:58 -05:00
7d07baa8ad
Better load balance fix_qeq_reax_kokkos for half neigh list
2017-12-21 11:07:51 -07:00
b9184ef441
Add special KOKKOS styles individually
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This avoids unnecessary dependencies
2017-12-20 04:51:46 -05:00
ff2b61354d
Bugfix for building LAMMPS+KOKKOS+DPD with CMake
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Resolves issue #753 , but there might be more work ahead.
2017-12-20 03:17:40 -05:00
18acc6ae47
remove some dead code
2017-12-19 15:01:11 -05:00
56e633a2cf
error out on trying to compile USER-INTEL with -DLAMMPS_BIGBIG
2017-12-19 14:54:35 -05:00
798d68c607
Edits to accelerate_kokkos.txt
2017-12-18 14:50:33 -07:00
46fe0a968b
Fix compiler warnings in atom_vec_hybrid_kokkos
2017-12-18 14:09:39 -07:00
00a9672524
Fix issue in fix_qeq_reax_kokkos, can't call child function from base constructor
2017-12-18 13:58:37 -07:00
a2756db66b
Update to Kokkos library v2.5.00
2017-12-15 16:42:06 -07:00
da83feb8ca
Merge branch 'master' into kk_update
2017-12-15 16:36:21 -07:00
a7bc3ed391
Add missing fences in comm_kokkos
2017-12-15 13:30:17 -07:00
68cf6941e1
Add Kokkos thread fences to pack/unpack routines
2017-12-15 13:01:38 -07:00
73c55ac4d1
Fix up docs after renaming
2017-12-15 14:06:16 -05:00
2a131d1416
Merge remote-tracking branch 'upstream/master' into fix_python_move
2017-12-15 13:56:54 -05:00
bcc5f49d0b
Rename fix python to fix python/invoke
2017-12-15 13:53:04 -05:00
950bfb84a9
Clean up after renaming back to fix python/move
2017-12-15 13:27:27 -05:00
4d725c3153
Revert "Rename fix python/move to move/python"
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This reverts commit 4d915dba08
2017-12-15 13:17:12 -05:00
10fa54b2fd
correct error messages. the atom style is called "smd" not "tlsph"
2017-12-13 18:44:31 -05:00
8a36cdc6bc
correct velocity output for write_data of atom style smd
2017-12-13 18:42:24 -05:00
e5cd068cd5
Merge branch 'patch-3' of https://github.com/abbatux/lammps into collected-bugfixes-and-updates
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This closes #745
2017-12-13 17:41:00 -05:00
cec22dda92
change pair style airebo/intel to compile with -DLAMMPS_BIGBIG
2017-12-13 16:20:49 -05:00
9a71efc5d5
fix neb bugfix from Emile Maras
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NEB was not working fine when using multiple proc
per replica and the keywords last/efirst or last/efirst/middle
I have corrected this in the enclosed fix_neb.cpp
I also slightly modified the nudging for this free end so that
it would be applied only when the target energy is larger than
the energy. Anyway if the target energy is lower than the energy,
the replica should relax toward the target energy without adding
any nudging.
I also modified the documentation according to this change.
2017-12-13 15:19:46 -05:00
2f857c6eda
correct fix neigh/history/omp to properly support -DLAMMPS_BIGBIG compilation
2017-12-13 15:12:14 -05:00
8a93f63de9
Update Kokkos docs
2017-12-13 10:05:53 -07:00
193252275f
A few more tweaks to charge history in fix_qeq_reax_kokkos
2017-12-12 09:54:28 -07:00
5968850306
Fix broken charge history in fix_qeq_reax_kokkos
2017-12-12 09:20:09 -07:00
3291a4fe96
Revert "no need to include library.o in the LAMMPS executable"
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This reverts commit 4a3a6b4455
2017-12-11 08:08:49 -05:00
1b07a4edee
Fix memory leak in pair python
2017-12-10 17:14:08 -05:00
16d6dfcab6
Bugfix for effective plastic strain rate calc
2017-12-08 11:40:44 +11:00
0edad83b25
Update atom_vec_smd.cpp
2017-12-08 11:29:12 +11:00
81a1c007ed
correct file name for doc file
2017-12-07 16:39:41 -05:00
0b51e9b2ff
add documentation for fix move/python
2017-12-07 16:36:36 -05:00
4b1bcaa1ae
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
ed8680d695
suspend support for sphinxcontrib.images
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the sphinxcontrib.image extension was broken with sphinx 16.x.
however, sphinx 15.x breaks with newer version of the multiprocessor module.
so we suspend the thumbnail processing and lift the lock to sphinx 15.x
also, the number of parallel sphinx tasks is can be overridden with SPHINXEXTRA="-j #'.
default is to try use all local CPU cores.
2017-12-07 15:38:15 -05:00
29df5a536f
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_es_RNG
2017-12-07 10:57:01 -07:00
d029cb9002
Merge pull request #743 from stanmoore1/kk_yukawa_fix
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Fix compile error in pair_yukawa_kokkos
2017-12-07 10:31:04 -07:00
3e99d1a83a
Add pair yukawa/kk to Section_commands
2017-12-07 09:06:33 -07:00
c4e83be533
Fix compile error in pair_yukawa_kokkos
2017-12-07 08:42:17 -07:00
d7e5d60f90
Merge pull request #738 from rbberger/pylammps_thermo_style_fix
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PyLammps bugfix to support custom thermo output with vector element addressing
2017-12-07 08:25:01 -07:00
5179efd2bb
Merge pull request #741 from stanmoore1/kk_compile
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Reduce Kokkos compile dependencies
2017-12-07 08:24:22 -07:00
abb2fe5be7
Merge pull request #740 from stanmoore1/improve_reax
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Improve ReaxFF
2017-12-07 08:23:47 -07:00
bae45e2493
Merge pull request #737 from akohlmey/collected-bugfixes
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Collected bugfixes and small updates for next patch
2017-12-07 08:23:06 -07:00
73d509f339
Merge pull request #735 from jaapkroe/extep
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Add ExTeP pair style
2017-12-07 08:22:34 -07:00
fa0c28b717
Merge pull request #731 from Pakketeretet2/pair-yukawa-kk
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Added a KOKKOS-enabled Yukawa pair style.
2017-12-07 08:21:20 -07:00
bc3a84b480
Merge pull request #727 from lammps/fix-gcmc-examples
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new example scripts for fix gcmc
2017-12-07 08:19:56 -07:00
4d915dba08
Rename fix python/move to move/python
2017-12-05 23:42:57 -05:00
f64544a5fe
Move instantiation of MemoryKokkos class
2017-12-05 08:34:24 -07:00
fc742eb2ef
Remove outdated elastic constants
2017-12-05 16:23:20 +01:00
1baecc689e
Merge pull request #3 from stanmoore1/kk_yukawa
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Add pair_yukawa_kokkos to Install.sh and minor cleanup.
These changes look fine. Sorry for the tabs, I must have forgotten about those.
2017-12-04 14:16:53 -05:00
d916416cc5
Add pair_yukawa_kokkos to Install.sh and minor cleanup
2017-12-04 12:02:32 -07:00
2813923f15
Add multiple inheritance to pair_multi_lucy_rx_kokkos
2017-12-04 10:43:41 -07:00
4a3a6b4455
no need to include library.o in the LAMMPS executable
2017-12-03 19:37:42 -05:00
f8891a4451
Rename fix python/integrate to python/move
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This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.
2017-12-02 01:04:46 -05:00
51688b2504
Improve performance of Python integrator (NVE_Opt version)
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Removing the loop over atoms by using NumPy array indexing allows to recover
performance close to that of plain fix nve.
2017-12-02 00:40:21 -05:00
93be2d264e
Detect correct integer type in lammps python interface
2017-12-02 00:39:15 -05:00
b9fd1156b2
Completed first version of fix python/integrate
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This includes an example of how to implement fix NVE in Python.
The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.
To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
2017-12-02 00:39:15 -05:00
bbfe16782b
Adjust .gitignore
2017-12-02 00:37:14 -05:00
1931d2088a
Started FixPythonIntegrate
2017-12-02 00:37:14 -05:00
5d9a6c1fe2
Add checks to Kokkos Install.sh so that files aren't unnecessarily recompiled
2017-12-01 16:06:50 -07:00
e7f97728c3
disable disruptive debug output
2017-12-01 17:14:11 -05:00
58ed92d905
one more file that doesn't require to include accelerator_kokkos.h
2017-12-01 16:45:22 -05:00
14aa036f36
add missing header files to USER-INTEL package
2017-12-01 15:53:02 -05:00
42e03da70c
Remove redundant #include in input.cpp
2017-12-01 13:16:35 -07:00
5d2e097b27
Need dynamic cast for multiple inheritance
2017-12-01 12:53:40 -07:00
da51a8a0bb
Add missing header files to GPU package
2017-12-01 12:13:14 -07:00
80dffb27e2
Add missing header files
2017-12-01 11:33:42 -07:00
5b33f153f4
Add newline to memory_kokkos.h
2017-12-01 10:33:47 -07:00
31eb12920c
Use multiple inheritance to remove accelerator_kokkos.h out of region.h and kspace.h
2017-12-01 10:18:22 -07:00
31f2ca1e4c
Use multiple inheritance to remove accelerator_kokkos.h out of pair.h
2017-12-01 09:51:40 -07:00
15a3364c2c
Make memory_kokkos its own class
2017-12-01 09:13:31 -07:00
c3aa705d04
Improve performance of pair_reaxc, this change is safe because the non-bonded i-loop doesn't include ghost atoms; this optimization is already included in the USER-OMP version
2017-11-30 09:22:32 -07:00
8c2d38c7e9
Remove non-existent function in reaxc_forces_omp
2017-11-30 09:13:03 -07:00
e3b961b622
Improve performance of PairReaxCKokkos
2017-11-30 09:10:39 -07:00
319508bd29
fix scoping ambiguity issue that confuses nvcc
2017-11-30 10:56:58 -05:00
6f7bd78ea2
Fixes issue #701
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PyLammps now supports thermo_style entries such as c_msd[4]
2017-11-29 01:06:44 -05:00
5647522906
various small cosmetic adjustments to increase conformance with LAMMPS programming conventions
2017-11-28 12:34:23 -05:00
e4b14213b4
delete old log files. new log files are approved by @athomps
2017-11-28 11:35:49 -05:00
fa6fc947f2
fix issues in FixNeighHistory and FixNeighHistoryOMP reported in https://sourceforge.net/p/lammps/mailman/message/36138319/
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This supersedes and closes PR #734
2017-11-28 11:28:15 -05:00
e1189381e0
correct documentation for create_atoms rotate
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This closes #736
2017-11-28 11:19:19 -05:00
39d24ab7eb
ExTeP potential file header update
2017-11-27 21:25:23 +01:00
5770a20e2c
added ExTeP to USER-MISC
2017-11-27 21:16:51 +01:00
83ec9815fe
Merge pull request #733 from pastewka/17_dump_nc3
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BUG: Proper handling of bigint data in NetCDF dump style. Affects LAMMPS version compiled with LAMMPS_BIGBIG.
2017-11-27 11:07:58 -07:00
90ee52296b
Merge remote-tracking branch 'andeplane/fix_ave_chunk_bug' into collected-bugfixes
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this closes PR #732
2017-11-27 11:45:09 -05:00
f02eb225c6
Merge branch '17_dump_nc3' of github.com:pastewka/lammps into 17_dump_nc3
2017-11-26 22:39:03 +01:00
a111cf640a
BUG: Proper handling of bigint data. Corrects behavior when compiled with LAMMPS_BIGBIG.
2017-11-26 22:35:56 +01:00
e755a8339d
BUG: openfile is called multiple times, second call stopped code with 'at keyword requires use of append yes'
2017-11-26 22:31:47 +01:00
f7f6a15ac0
MAINT: Removed superfluous code.
2017-11-26 22:31:47 +01:00
36b7aa73aa
MAINT: Use proper data type for bigint when defining NetCDF file.
2017-11-26 22:31:47 +01:00
9a5723123f
Set peratom_freq in fix ave/chunk
2017-11-21 23:43:52 -08:00
7d07f062b6
Remove const from variable
2017-11-20 10:21:19 -07:00
f3ed148828
Fix for big endian machines
2017-11-20 10:18:53 -07:00
5ba80662c3
Undid the removal of rad in pair_yukawa.
2017-11-17 15:07:59 -05:00
53c1558271
Updated docs for pair_yukawa
2017-11-17 14:21:54 -05:00
8e5d4fa891
Added a KOKKOS-enabled Yukawa pair style.
2017-11-17 14:12:16 -05:00
e55c90cc44
Moved rerun bug fix to individual affected styles
2017-11-14 14:01:07 -05:00
ec067bde36
fix cut-n-paste error in create_bond docs
2017-11-13 17:59:16 -05:00
751465aad3
Merge branch 'master' into cluster-fragment-aggregate-fixes
2017-11-13 14:32:26 -05:00
adbc75cae6
add alternate log files with the latest version of LAMMPS
2017-11-13 11:52:01 -05:00
dde94c28a7
new example scripts for fix gcmc
2017-11-13 09:07:25 -07:00
f2dc764d1d
Merge pull request #723 from lammps/replicate_bbox
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Add bounding box to Replicate command
2017-11-13 09:01:38 -07:00
c4c59b909e
Merge pull request #716 from akohlmey/collected-small-changes
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Collected small changes and bugfixes for next patch
2017-11-13 09:00:26 -07:00
e2e21f0661
Merge pull request #714 from Pakketeretet2/user-manifold-plane-wiggle-fix
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User manifold plane wiggle fix
2017-11-13 08:59:40 -07:00
6abf68f614
Merge pull request #712 from akohlmey/linalg-for-latte
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Update lib/linalg for use with lib/latte
2017-11-13 08:59:18 -07:00
a97553a92e
Merge pull request #709 from abbatux/patch-1
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Update pair_smd_tlsph.cpp
2017-11-13 08:58:29 -07:00
dbd4acc4d6
Merge pull request #708 from abbatux/patch-2
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Update smd_material_models.cpp
2017-11-13 08:58:07 -07:00
a085ee0c55
Always build occasional lists on first step
2017-11-13 04:53:16 -05:00
c16b7a3273
Multiple run fix for cluster/aggregate computes
2017-11-12 15:57:53 -05:00
858065029d
Reverse communication compute fragment/aggregate
2017-11-12 15:57:02 -05:00
40e776ebc6
Remove OpenMP from KOKKOS_DEVICES in Kokkos CUDA Makefiles since normally this doesn't improve performance
2017-11-10 09:55:11 -07:00
f043212511
USER-DPD: fix a segfault when using constant temperature (DPD vs. DPDE)
2017-11-07 13:57:29 -06:00
4342bcdafc
Fix CUDA issue in USER-DPD/random_external_state.h
2017-11-07 09:17:58 -07:00
2e40c00995
add option to the print command to also print to the global universe screen and logfile
2017-11-07 10:00:57 -05:00
f39c6213e1
Change path to nvcc_wrapper
2017-11-06 13:50:16 -07:00
88474fc5c2
Remove Kokkos tpls directory
2017-11-06 13:48:26 -07:00
16b5315845
Update Kokkos to v2.04.11
2017-11-06 13:47:33 -07:00
e337db4059
Replicate bbox from Chris Knight
2017-11-06 11:31:43 -07:00
ba43465268
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2017-11-06 13:30:08 -05:00
09c61ca598
correct listing of USER-OMP variants of fix rigid styles
2017-11-06 13:29:59 -05:00
0f971bf07c
print name of unknown or incorrect variable in error message
2017-11-06 10:41:32 -05:00
5a8c5eb479
provide last input command line with error->one() output
2017-11-06 10:41:01 -05:00
aa0d6cd75b
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2017-11-04 02:49:28 -04:00
b34000a5e1
make *_gpu_reinit() functions consistent in returning void. correct prototypes in src/GPU, too.
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this supersedes and closes #719
2017-11-04 02:49:22 -04:00
279339ebd0
Remove the now unused AIRct_ssa[] array from the NeighList class.
2017-11-03 13:42:36 -05:00
605fe53c07
USER-DPD: make the kokkos and non-kokkos fix_shardlow match more closely
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This was accomplished with several key changes:
1) Modified fix_shardlow's control flow to match fix_shardlow_kokkos so
that random numbers are pulled fromn the RNGs in exactly the same order.
2) Created random_external_state.h, a simplified version of the Kokkos
random number generator that keeps its state variables external to itself.
Thus it can be used both with and without Kokkos enabled, as long as the
caller stores and passes in the required state variable.
3) Replaced all references to random_mars.h and Kokkos_Random.hpp code in
the fix_shardlow* files with calls to the random_external_state.h code,
guaranteeing that fix_shardlow* is using an identical RNG in all cases.
Result: most (56 of 61) of our internal tests now generate the same results
with kokkos turned on or off. Four cases still differ due to what appear
to be vectorization caused rounding differences, and the fifth case
appears to be something triggered by the kokkos "atom_style hybrid" code.
2017-11-03 12:51:37 -05:00
65b77230fd
added missing "dihedral" in compute dihedral/local docs
2017-11-02 15:04:04 -04:00
91e4bcca33
BUG: openfile is called multiple times, second call stopped code with 'at keyword requires use of append yes'
2017-11-01 21:28:14 +01:00
7ef17efe2e
MAINT: Removed superfluous code.
2017-11-01 21:20:19 +01:00
8a804460f9
MAINT: Use proper data type for bigint when defining NetCDF file.
2017-11-01 21:19:55 +01:00
f6658d10b7
fix incorrect create_atoms example for selecting created atoms with a variable
2017-10-30 23:33:26 -04:00
f4d0aa3393
correct cut-n-paste bug reported by Massimo Pica Ciamarra on lammps-users
2017-10-27 11:25:57 -04:00
99a6c6edb4
Fixed a typo in manifold plane wiggle.
2017-10-26 12:33:16 -04:00
a26ffc7ff7
Reset plane wiggle in master.
2017-10-26 12:32:30 -04:00
b002e071e7
Reset some files back to upstream.
2017-10-26 12:31:30 -04:00
9f44e3e5b0
Merged upstream.
2017-10-26 12:26:34 -04:00
e79cd6c62c
Moved some stuff around.
2017-10-26 12:25:55 -04:00
82c6fd609e
Merge branch 'master' of https://www.github.com/lammps/lammps
2017-10-26 12:06:57 -04:00
2dbb44f2c6
provide Makefile.lammps template for use with bundled linalg lib
2017-10-24 13:38:04 -04:00
d1630bbe34
add missing BLAS/LAPACK functions used by LATTE to linalg lib
2017-10-24 13:22:20 -04:00
941ee565a1
Added lal_ufm_ext.cpp in lib/gpu
2017-10-24 11:12:51 -02:00
b63acf6843
Added the UFM files (doc/src - lib/gpu - src)
2017-10-24 11:11:10 -02:00
41c25877e8
Update smd_material_models.cpp
...
The pressure pFinal using ShockEOS() was of the wrong sign when Gamma = 0.
2017-10-24 11:04:11 +11:00
39df9f5d94
patch 23Oct17
2017-10-23 16:07:21 -06:00
68d04119d3
Merge pull request #707 from akohlmey/granular-omp-refactor
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Updated neighbor list history processing for USER-OMP
2017-10-23 13:35:43 -06:00
0148c2ac81
updated neighbor list history processing for USER-OMP
2017-10-23 14:12:19 -04:00
253a17b6d0
Update pair_smd_tlsph.cpp
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Correction of a typo in the computation of LAME_LAMBDA.
2017-10-23 12:45:58 +11:00
a7ad12491f
Merge pull request #706 from lammps/doc-cs
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update to doc pages for new coreshell pair styles
2017-10-21 16:12:23 -06:00
2137be3219
update to doc pages for new coreshell pair styles
2017-10-21 15:50:27 -06:00
ce78f6943d
Merge pull request #705 from akohlmey/fix_rigid_bugfix
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fix segfault bug in fix rigid/small found by regression testing
2017-10-20 17:01:50 -06:00
998aedc6c1
Merge pull request #670 from vishalkenchan/pair_style/coul_wolf_cs
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add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package
2017-10-20 16:09:33 -06:00
0a02c3c78c
fix segfault bug for in fix rigid/small found by regression testing
2017-10-20 16:56:06 -04:00
aaf5e87c84
Merge pull request #703 from akohlmey/custom-rigid-body-generation
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Allow rigid body generation from custom properties
2017-10-20 14:08:15 -06:00
2d0f5e277c
Merge pull request #704 from akohlmey/bond-gromos-bugfix
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Compute energy correctly for bond style gromos
2017-10-20 14:06:35 -06:00
260bbc6f9f
Merge pull request #702 from giacomofiorin/colvars-fix-the-fix
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Fix a Colvars error that was hidden by the previous segfault
2017-10-20 14:06:15 -06:00
6b34a30528
compute energy correctly for bond style gromos
2017-10-20 14:53:22 -04:00
83c7d3a1d2
update fix rigid documentation
2017-10-20 14:18:50 -04:00
961b976374
add/correct code to define rigid bodies with atomstyle/atomfile variables and via custom per-atom properties
2017-10-20 13:56:09 -04:00
ac6434e496
add input examples for custom rigid body definition
2017-10-20 13:54:45 -04:00
f479f02589
Fix a Colvars error that was hidden by the previous segfault
2017-10-20 13:41:31 -04:00
e284545c5b
added some documentation and reference example
2017-10-20 12:03:22 +02:00
e368acdaeb
Merge pull request #700 from giacomofiorin/colvars-fix
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Import segfault fix in Colvars module
2017-10-19 11:45:36 -06:00
6e7504f153
Import segfault fix in Colvars module
2017-10-19 08:09:44 -04:00
71c4edda51
add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package
2017-10-19 13:21:13 +02:00
b0b67ca610
Merge branch 'master' into master
2017-10-18 18:49:15 -04:00
40147a7a64
Merge pull request #699 from lammps/doc-update2
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cross ref fix deform and new fix nvt/uef in doc pages
2017-10-18 16:44:18 -06:00
f709a723cd
cross ref fix deform and new fix nvt/uef
2017-10-18 15:26:15 -06:00
6dd55e49cb
Merge pull request #698 from lammps/doc-update
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small updates to recently added docs and rename of an example dir
2017-10-18 15:24:54 -06:00
281b1dc375
small updates to recently added docs and rename of an example dir
2017-10-18 14:56:47 -06:00
e93f8f8889
Merge pull request #671 from danicholson/user-uef
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USER-UEF package for extensional flow
2017-10-18 13:38:56 -06:00
35f2cfa0bf
Merge pull request #669 from urpedersen/master
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fix rhok - biasing long-range order
2017-10-18 13:31:15 -06:00
e44196c011
Merge pull request #694 from akohlmey/bond-gromos
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Add gromos bond style
2017-10-18 13:27:15 -06:00
2fe1d1b904
Merge pull request #697 from andeplane/fix_heat_bug
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Avoid checking region when not specified
2017-10-18 13:26:19 -06:00
b1b4a52b14
Merge pull request #695 from timattox/USER-DPD_small_updates
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USER-DPD small updates
2017-10-18 13:25:48 -06:00
382de50341
Merge pull request #696 from wmbrownIntel/intel-update-oct17
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Bug fix for unexpected case where a Intel bonded style is specified but there are no types
2017-10-18 13:25:07 -06:00
7dfc6b7eab
Merge pull request #688 from lammps/history
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refactoring of neighbor history
2017-10-18 13:24:36 -06:00
19eb5d3897
Avoid checking region when not specified
2017-10-18 18:05:34 +02:00
17c17ac409
update multi-threaded neighbor list build for neighbor list refactor
2017-10-18 11:25:15 -04:00
39ededd46c
update respa/omp integrator style for neighbor list refactor
2017-10-18 11:24:44 -04:00
2c7528811d
update several pair styles to be compliant with refactored respa lists data structures
2017-10-18 11:24:12 -04:00
0966e14e73
more changes to rRESPA neighbor lists
2017-10-17 17:33:01 -06:00
bb141aaae0
USER-INTEL: Bug fix for case where a bond/angle/dihedral/improper style is specified, but there are no bond/... types and therefore no allocation.
2017-10-16 22:51:56 -07:00
374d619769
add gromos bond style
2017-10-16 14:57:12 -04:00
59de1a71c8
Merge branch 'history' of github.com:lammps/lammps into history
2017-10-16 14:37:30 -04:00
4c6779cb0d
USER-DPD Kokkos: propagate the new neigh_modify options from efaa4c67
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Propogate the efaa4c67
2017-10-16 13:37:27 -05:00
5fb5f70ec6
update USER-OMP code for shear history neighbor refactoring
2017-10-16 14:37:20 -04:00
b0bba1976b
USER-DPD: remove unused coord2bin() variants, and add ISFINITE checks
2017-10-16 13:36:44 -05:00
f8f13d929f
Merge pull request #693 from giacomofiorin/colvars-update
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Update Colvars to version 2017-10-11
2017-10-13 17:25:06 -06:00
3e89b270fd
Update Colvars to version 2017-10-11
...
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics. Also included are several small fixes.
Below is a list of relevant commits in the Colvars repository since the last update.
321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
f6ddc8c7c9
Fix compile errors from neigh history refactor
2017-10-13 10:49:31 -06:00
a973c65d67
Merge pull request #691 from akohlmey/collected-fixes
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Collected small changes for next patch
2017-10-13 09:50:03 -06:00
1a200588bd
Merge pull request #689 from rbberger/pylammps_autocomplete_fix
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Limit IPython autocomplete to known commands and properties
2017-10-13 09:49:03 -06:00
18ca2292c2
Merge pull request #686 from giacomofiorin/lepton-library
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Add Lepton library within lib/colvars
2017-10-13 09:48:42 -06:00
d3ef4bd594
Merge pull request #685 from ellio167/kim-api-v1.9.2
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Update lib/kim for kim-api-v1.9.2
2017-10-13 09:48:16 -06:00
3df9caf435
drop const qualifier to allow bracketing of lookup index
2017-10-13 10:29:49 -04:00
fa2e5ac2d9
handle lookup exceptions consistently across energy and energy+force lookup in bond/angle style table
2017-10-13 10:13:34 -04:00
b7c7492608
handle invalid lookup for bond/angle tabulation
2017-10-13 09:50:56 -04:00
cee94da85e
bugfix. avoiding operating on uninitialize data. closes #690
2017-10-13 00:15:15 -04:00
45aa7de171
Limit IPython autocomplete to known commands and properties
2017-10-12 14:43:17 -04:00
53aa92cfaf
add support for neighbor list history refactoring in USER-OMP part 2
2017-10-11 10:30:29 -04:00
7e35042c42
add support for neighbor list history refactoring in USER-OMP part 1
2017-10-11 10:29:41 -04:00
01051e4cb1
refactoring of neighbor history
2017-10-10 16:53:51 -06:00
d90aad887e
Add Lepton library within lib/colvars
2017-10-09 15:25:43 -04:00
775a15b9da
Update lib/kim for kim-api-v1.9.2
2017-10-09 14:06:30 -05:00
93c9a92743
Merge pull request #684 from irisTa56/bugfix-in-domain.cpp
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Bugfix for checking image flags
2017-10-09 08:30:48 -06:00
14dc1c698c
Merge pull request #683 from wmbrownIntel/pppm_intel_fix
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Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
2017-10-09 08:29:52 -06:00
a1f5693fe0
Merge pull request #681 from lammps/dump-modify
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remove dependence of dump modify 'at' and 'append'
2017-10-09 08:29:12 -06:00
534b7adde4
Bugfix for checking image flags
2017-10-09 21:29:07 +09:00
02646100e9
correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in PR #681 review
2017-10-09 07:49:29 -04:00
7e58f084d2
Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
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This commit simplifies the code by eliminating packing optimizations that were slower
under typical parameters and had some memory bugs.
2017-10-08 08:33:07 -07:00
0f5d7dcc0f
cmake: added USER-UEF
2017-10-07 12:38:41 -06:00
b6187173e6
Merge branch 'master' into HEAD
2017-10-07 12:35:51 -06:00
88a33edb50
Merge pull request #680 from lammps/map-yes
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add atom_modify map yes, also timers to create_atoms and replicate
2017-10-06 17:43:52 -06:00
6820db99e2
avoid merge conflict
2017-10-06 14:41:38 -04:00
58e1969de2
rename misleading "CPU time" into "Time spent"
2017-10-06 14:34:10 -04:00
e91e505fb3
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -06:00
f7cbdcf995
Merge pull request #673 from pastewka/17_dump_nc2
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Multi file support for NetCDF dump style
2017-10-06 09:14:12 -06:00
4cfa88b70f
Merge pull request #674 from wmbrownIntel/user-intel-update
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Mike Brown has added DPD to the USER-INTEL package with speedups over 3X for Xeon Phi and over 1.7X for some Xeon processors.
2017-10-06 09:12:39 -06:00
352a20fc1c
DOC: Updated doc to separate description of 'append' and 'at' keywords.
2017-10-06 16:38:15 +02:00
dc0e20947e
MAINT: Return error when 'at' keyword is used without 'append yes'.
2017-10-06 16:37:52 +02:00
05847a0e87
Merge branch 'master' into user-intel-update
2017-10-06 10:18:38 -04:00
439c2fd980
Merge pull request #677 from stanmoore1/kk_update
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Update to Kokkos r2.04.04 and add workaround for performance regression
2017-10-05 17:10:00 -06:00
15853a0e38
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
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Add Kokkos threaded reverse communication
2017-10-05 17:08:49 -06:00
bd17ee5df7
Merge pull request #675 from wesbarnett/master
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cmake: Add -restrict for Intel compilers
2017-10-05 17:08:35 -06:00
a9b7ff1154
Merge pull request #679 from stanmoore1/kk_reax_comm
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ReaxC optimizations
2017-10-05 17:08:17 -06:00
0dd7ba26c0
Merge pull request #672 from akohlmey/phana-w-tricubic
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Streamline compilation of "phana" tool for fix phonon
2017-10-05 17:01:37 -06:00
7a90eef527
Merge pull request #668 from ovilab/modify_deallocation_fix
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Fixed proper deletion of fixes if fix is NULL
2017-10-05 17:00:10 -06:00
5d0626e50e
Merge pull request #665 from akohlmey/collected-small-fixes
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Collected small fixes
2017-10-05 16:58:49 -06:00
4b7ca0383a
Merge pull request #664 from timattox/kokkos_atom2bin
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Kokkos atom2bin
2017-10-05 16:58:16 -06:00
0ed987dc61
Merge pull request #663 from jdevemy/master
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Authorize hybrid/overlay for fix srp
2017-10-05 16:56:20 -06:00
55a3fdca80
Merge pull request #660 from junghans/latte_fix
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cmake: fix build with system latte
2017-10-05 16:55:22 -06:00
214c0cfb2b
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
e0efdd50fa
Switch to classic comm if ghost_velocity. The check_forward and check_reverse tests aren't necessary because the fix/pair/etc. comm is done in a separate routine.
2017-10-05 15:47:46 -06:00
44d2e8ff74
Add pre_reverse to verlet_kokkos and comment out timer
2017-10-05 15:28:35 -06:00
6bf2c60c07
Fix issues in Kokkos comm
2017-10-05 14:58:05 -06:00
eecd2fbaee
Remove hardcoded value in fix_qeq_reax
2017-10-05 11:23:31 -06:00
2b0bfcb10f
Fix memory leak in pair_reaxc_kokkos
2017-10-05 10:35:09 -06:00
3653f40120
Reduce unnecessary communication in fix_qeq_reax
2017-10-04 12:10:13 -06:00
bda0ee3aa1
Destroy unneeded fix in pair_reaxc_kokkos
2017-10-04 12:06:03 -06:00
957263431a
Ensure consistency with documentation
2017-10-04 09:38:43 +02:00
f12031f84d
add support for building rigid bodies from custom atom properties or atom style variables
2017-10-04 01:14:57 -04:00
c522b1b7a9
add call to fftw_cleanup() before exiting to avoid bogus leak reports when compiling with FFTW v3.x
2017-10-04 00:22:56 -04:00
a55adf4a68
Update to Kokkos r2.04.04 and add workaround for performance regression
2017-10-03 11:30:00 -06:00
2876baafd0
Use -restrict whenever Intel is used, no matter the package
2017-10-03 13:08:56 -04:00
ca032f21fb
Add Kokkos threaded reverse comm option
2017-10-03 10:14:24 -06:00
197f082784
cmake: Add -restrict for Intel compilers for some packages
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Some packages (USER-OMP, OPT, and USER-INTEL) require the -restrict
flag when using the Intel compiler.
2017-10-03 11:28:33 -04:00
1bb7af9ef9
integrate fix rhok into the LAMMPS source code management and documentation system
2017-10-03 10:45:08 -04:00
251f28049a
make fix rhok more similar to other LAMMPS sources
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- re-indent to 2 blanks
- white space cleanup
- use force->numeric() and force->inumeric() instead of atof() and atoi()
- include system headers before local LAMMPS headers
2017-10-03 10:10:38 -04:00
f07719e924
make fix rhok examples more consistent with LAMMPS conventions:
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- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
2017-10-03 10:08:38 -04:00
5f527091b8
Update readme.md
2017-10-03 12:02:01 +02:00
30aaa7e47b
Update readme.md
2017-10-03 12:00:43 +02:00
74dcf0bf9b
Update readme.md
2017-10-03 11:54:46 +02:00
e9b07a7a10
Update readme.md
2017-10-03 11:52:48 +02:00
fd8f5f8f9e
Update readme.md
2017-10-03 11:52:08 +02:00
5c59eb637b
Update readme.md
2017-10-03 11:49:57 +02:00
250ef9f837
Update readme.md
2017-10-03 11:46:08 +02:00
e44f370d49
Update readme.md
2017-10-03 11:44:52 +02:00
1e790fbafe
Update readme.md
...
Now use the standard namings.
Corrected spelling errors.
2017-10-03 11:44:23 +02:00
35cc795972
Update in.setup
2017-10-03 11:17:43 +02:00
245bf74552
Rename setup.lmp to in.setup
2017-10-03 11:16:54 +02:00
7e8bbe8481
Rename pinning.lmp to in.pinning
2017-10-03 11:16:29 +02:00
e6d687faac
Rename crystal.lmp to in.crystal
2017-10-03 11:15:49 +02:00
8a2cf5ce8e
reformatting and use citeme class
2017-10-03 11:13:10 +02:00
8f79f5ddb9
add the LAMMPS copyright
2017-10-03 10:59:46 +02:00
40ae6f215b
add the usual LAMMPS copyright
2017-10-03 10:58:21 +02:00
4dcc49ebe2
Delete fix_rhok.cpp
2017-10-03 10:56:07 +02:00
fe14eeccac
Delete fix_rhok.h
2017-10-03 10:54:22 +02:00
9dc42fd4db
intel_simd.h is currently also needed by dihedral/charmm, not just sw.
2017-10-02 23:53:05 -07:00
5e89269631
Minor adjustments to intel makefiles and documentation based on the reversed
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preprocessor logic and default memory align. Removing knl_coprocessor makefile.
2017-10-02 23:41:14 -07:00
11eed234f0
include dump cfg/uef in commands toctree
2017-10-03 00:14:34 -04:00
af1fc45db0
added citation to doc
2017-10-03 00:04:52 -04:00
b34109af60
formatting changes
2017-10-02 23:43:31 -04:00
1dffb0cf82
reran npt_biaxial examples
2017-10-02 23:27:10 -04:00
588b2534c9
Minor fix for FixNHUef constructor
2017-10-02 23:26:21 -04:00
d2aa05cb36
update README in USER-INTEL for recent LRT logic reversal
2017-10-02 21:24:51 -04:00
466fde6443
update documentation for the reversal in the INTEL_MKL_RNG define
2017-10-02 21:20:26 -04:00
2a24cbfe0c
reverse logic for using MKL pRNG: this way, make serial and make mpi will compile LAMMPS with USER-INTEL installed
2017-10-02 21:13:51 -04:00
00aef0fe00
rerun logfiles for USER-UEF example inputs
2017-10-02 17:40:46 -04:00
92d9b361fc
include USER-UEF styles in PDF version of manual
2017-10-02 17:39:59 -04:00
8acdc8020d
add USER-UEF classes to .gitignore
2017-10-02 17:24:36 -04:00
cc09a633a2
small code refactor for FixNHUef class
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- use forward declaration for UEFBox to avoid having to include custom header
- remove uef_arg_kludge() thanks to changes in 0c7879e902
2017-10-02 17:19:42 -04:00
81be9b37de
formatting, whitespace and include file/constants cleanup
2017-10-02 17:15:13 -04:00
0c7879e902
provide compatibility entries in FixNH option parsing for new USER-UEF package
2017-10-02 16:31:41 -04:00
8d384b9149
whitespace cleanup
2017-10-02 15:03:48 -04:00
529eeb6039
Reduce GPU data transfer
2017-10-02 09:31:39 -06:00
cf24dd0265
Adding pair style dpd/intel and dihedral style fourier/intel
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Adding raw performance numbers for Skylake xeon server.
Fixes for using older Intel compilers and compiling without OpenMP.
Fix adding in hooks for using USER-INTEL w/ minimization.
2017-10-02 04:53:17 -07:00
a7b0d1f521
DOC: Corrected syntax for appending at certain frame (NetCDF only)
2017-10-01 14:40:19 +02:00
fbe42cda2d
MAINT: Only set append flag when not in multifile mode.
2017-10-01 14:31:33 +02:00
da7be99cc4
DOC: Added multi file example.
2017-10-01 14:28:20 +02:00
56d21bfb05
MAINT: Removed obsolete prmtop writer.
2017-10-01 14:22:04 +02:00
100231bba8
ENH: Enable multi file writes.
2017-10-01 14:21:09 +02:00
84378f8ae2
MAINT: Renamed _put_var1_x to _put_var1_bigint
2017-10-01 14:05:12 +02:00
6e342d2e45
MAINT: bigint (int64) maps onto either long or long long, depending on platform. Automatically choose the correct one.
2017-10-01 14:03:52 +02:00
091d058090
Fix typo
2017-09-30 17:44:15 -04:00
4c71beb024
cleanup/simplification of compilation for fix phonon analysis tool "phana"
...
- include the used tricubic functions directly as static functions
- silence compiler warnings
- define f2c.h imported data types directly or use C equivalents
- since the direct LAPACK API was called and not cLAPACK, declare LAPACK interface and depend only on LAPACK
- add proper dependencies
- disable automatic minor version number generation. step version manually.
- comment out optional spglib functionality by default
2017-09-30 12:12:15 -04:00
a86572f4fc
Reduce memory churn in Kokkos package
2017-09-29 16:20:19 -06:00
4524b0fa83
rename arg_kludge to uef_arg_kludge
2017-09-29 16:54:46 -04:00
4ef63feea7
reran examples
2017-09-29 15:50:31 -04:00
9f2740b7f1
Partially revert 01d0a5c, avoid atomics, safe because of the while loop. Worst case is the resize will happen again because max wasn't accurate
2017-09-29 13:41:35 -06:00
2a06b75af8
doc revisions
2017-09-29 15:36:41 -04:00
d7aac2fed5
Add sync/modify to nbin_kokkos
2017-09-29 13:26:02 -06:00
d898afaafb
use <> for system includes not ""
2017-09-29 09:19:38 -04:00
c66ddf9ac0
Update fix_rhok.txt
2017-09-29 08:03:02 +02:00
a64040ce2d
citeme
2017-09-28 18:33:04 -04:00
480b087c93
doc edits, README, and citeme
2017-09-28 18:31:51 -04:00
0029583463
doc edits i missed in earlier commit
2017-09-28 17:46:39 -04:00
c0f1a32661
fixed namespace issue
2017-09-28 17:43:59 -04:00
80898b8695
first draft of doc done
2017-09-28 17:42:02 -04:00
855b6000ef
initial commit. doc is in the works
2017-09-28 16:34:18 -04:00
285a123c90
Update fix_rhok.cpp
2017-09-28 18:42:15 +02:00
0f52dd7c5f
Update fix_rhok.h
2017-09-28 18:41:06 +02:00
10d1741e7f
Update fix_rhok.txt
2017-09-28 18:38:25 +02:00
d11733d3a0
typo in equation
2017-09-28 18:28:46 +02:00
348c4eb7f3
add .cpp and .h to root src
2017-09-28 18:18:28 +02:00
75b3f34a58
Update documentation
2017-09-28 18:16:06 +02:00
fe80c57bde
more documentation
2017-09-28 17:01:12 +02:00
e49f0e396b
Create fix_rhok.txt
2017-09-28 16:24:26 +02:00
37e55a825b
Create fix_rhok.txt
2017-09-28 16:20:03 +02:00
67e48264d9
Update fix_rhok.cpp
2017-09-28 16:02:20 +02:00
4e1eeca869
Update fix_rhok.cpp
2017-09-28 16:02:00 +02:00
2fda041972
Update fix_rhok.cpp
2017-09-28 16:00:16 +02:00
34c1adb4dd
Merge https://github.com/lammps/lammps
2017-09-28 12:28:58 +02:00
23e283f135
Fixed proper deletion of fixes if fix is NULL
2017-09-27 16:20:07 +02:00
de45fa6e71
correct bogus links in LATTE docs
2017-09-26 18:25:37 -04:00
bfdc4acb8b
add missing entry for pdf version of manual
2017-09-26 16:53:36 -04:00
fd3ecd0481
fix typo in formatting
2017-09-26 16:52:24 -04:00
8bba6d3e8c
correct formatting and broken/colliding link issues with LATTE package related documentation
2017-09-26 16:52:10 -04:00
53e4ee4f2d
need to re-init timers after initial setup
2017-09-25 23:20:42 -04:00
b60cff7e77
USER-OMP package depends on USER-DRUDE
2017-09-25 23:15:49 -04:00
38530415c8
-ltbbmalloc is required
2017-09-25 20:03:53 -04:00
0573aaa6da
update src/.gitignore for LATTE package
2017-09-25 19:37:55 -04:00
e6969002ce
having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc
2017-09-25 19:37:37 -04:00
0448bc9caf
Merged stuff.
2017-09-25 18:31:32 -04:00
836a6d292c
whitespace fixes, silence compiler warning about too few format specifiers
2017-09-25 16:31:39 -04:00
32e0de7a67
first pass at implementing atom2bin for KOKKOS neighbor lists
2017-09-25 14:06:20 -05:00
789812ec3d
KOKKOS: minor typo fix
2017-09-25 14:06:20 -05:00
88a882b457
Added reference to fix rhok implimentation
2017-09-25 18:59:23 +02:00
f1aea57e30
Update readme.md
2017-09-25 18:48:21 +02:00
b35f2ff8b4
Example of Interface Pinning Computation
2017-09-25 18:44:24 +02:00
4beccf508f
Move fix to USER-MISH
2017-09-25 18:35:53 +02:00
78a486c0fd
Authorize hybrid/overlay for fix srp
2017-09-25 16:18:08 +02:00
f2c1172741
patch 22Sep17
2017-09-22 15:46:34 -06:00
d6316c40d9
cmake: fix build with system latte
2017-09-22 15:36:14 -06:00
bcde318ccb
Merge pull request #659 from stanmoore1/kk_border_comm
...
Enhance Kokkos communication logic
2017-09-22 13:47:44 -06:00
3ed39ca844
Make Kokkos comm give warning and switch to classic comm instead of erroring out
2017-09-22 13:03:24 -06:00
ee487ef4aa
Merge pull request #652 from junghans/latte
...
Add LATTE fix
2017-09-22 10:32:19 -06:00
a8ae886667
update fix latte examples and virial
2017-09-21 10:40:54 -06:00
fe8244c1c2
Rename fix
2017-09-21 16:49:46 +02:00
3381a43378
Added readme.m
2017-09-21 16:20:06 +02:00
73708b091c
Added readme file, and removed old files
2017-09-21 16:17:26 +02:00
9a9af2ca5e
Delete README
2017-09-21 13:58:51 +02:00
491d5f3410
Added USER-PINNING package
2017-09-21 11:38:59 +02:00
5e35ab251b
fixed sucrose
2017-09-20 17:11:49 -06:00
d708e34ba6
cmake: download/build latte if not found
2017-09-20 12:01:26 -06:00
638b91bf74
Merge pull request #657 from lammps/snap-potentials
...
new SNAP potentials and examples
2017-09-20 09:34:51 -06:00
ad25a95297
whitespace cleanup
2017-09-20 11:13:13 -04:00
e7d042ba1a
convert DOS/Windows CR-LF line endings to native format
2017-09-20 11:12:58 -04:00
dd49d54889
new SNAP potentials and examples
2017-09-20 08:54:30 -06:00
fbaa7ab8fa
Merge pull request #655 from akohlmey/fixes-for-patch
...
collected small bugfixes for the next patch release
2017-09-20 08:51:47 -06:00
2e9803efb3
Merge pull request #645 from akohlmey/kokkos-makefile-updates
...
Some small kokkos makefile updates
2017-09-20 08:40:20 -06:00
59d2e13d48
add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other libraries
2017-09-19 19:06:02 -04:00
76d93f21dd
add fix latte command to doc pages
2017-09-19 16:55:08 -06:00
ac897ea645
LATTE package doc update and some small code changes
2017-09-19 16:27:25 -06:00
19f1f3a3e0
correct USER-INTEL installer script for verlet_lrt_intel files
2017-09-19 11:48:27 -04:00
be96486d66
compile all objects in the GPU library with -fPIC for building shared object
2017-09-19 11:24:48 -04:00
48dd824b26
ignore generated header files with OpenCL kernels
2017-09-19 11:24:38 -04:00
cdb6ec7419
reverse the pre-processor logic of the LRT mode define
...
with this change, the USER-INTEL package can be installed and
compiled without having to alter makefiles for adding -lpthread.
All "intel optimized" makefiles have been updated to have the
LRT feature enabled. This change will allow us to include the
USER-INTEL package in several automated testing configurations
and thus allows to detect incompatibilities and compilation issus faster.
2017-09-19 11:24:05 -04:00
aad8cd10ff
allow fix viscous to be used with dynamic groups
2017-09-18 18:08:57 -04:00
1ac90815f3
fix external only needs to collect virial in case it is requested
2017-09-17 23:59:34 -04:00
5f1842829e
activate virial contribution in fix lb/rigid/pc/sphere by default and protect virial computation with evflag
2017-09-17 21:10:41 -04:00
66130f5557
whether virial contributions from fixes are included depend on thermo_virial, not virial_flag.
2017-09-17 20:50:22 -04:00
388eab5eeb
correctly initialize thermo_virial in fix poems and protect access to vflag_XXX by checking for evflag !=0
2017-09-17 20:49:41 -04:00
a500048c9c
remove bogus version of temper/npt command
2017-09-17 19:25:22 -04:00
b4ecad7fbf
remove another couple of purge items from long ago
2017-09-17 19:22:43 -04:00
b5894e2190
automatically call 'make purge' before calling 'make package-update' or 'make package-overwrite'
2017-09-17 19:19:45 -04:00
6f1935ea40
correct embarrassing typo
...
this always happens after too much exposure to fortran codes. :-(
2017-09-15 21:58:47 -04:00
02665e45a4
fix doc in lib/latte/Makefile.lammps.*
2017-09-15 17:52:14 -06:00
cc2a53a8da
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into latte
2017-09-15 17:43:48 -06:00
d614d56c34
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
2017-09-15 17:41:02 -06:00
39daf3c6f6
added fix_latte.txt
2017-09-15 17:40:34 -06:00
17aeccf19f
Merge remote-tracking branch 'origin/master' into latte
2017-09-15 16:18:13 -06:00
d101fe3e79
Merge pull request #649 from akohlmey/fix-virial-aidan
...
Add support for selected fixes to optionally contribute to the virial
2017-09-15 15:25:09 -06:00
27f99534ec
Merge pull request #654 from giacomofiorin/colvars-small-fix
...
Fix small typo to calculation of accumulated work in Colvars
2017-09-15 15:22:09 -06:00
5f6937dadd
Merge pull request #653 from jdevemy/master
...
Bugfix for the limit keyword
2017-09-15 15:21:53 -06:00
3b39694f23
Merge pull request #628 from lammps/cmake_improvements
...
CMake improvements
2017-09-15 15:19:46 -06:00
99e5dc7104
add support for fix_modify virial yes to fix smd
2017-09-15 01:21:16 -04:00
ccb67d8dc5
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
2cd7cbd964
correct cut-n-paste error, add docs
2017-09-15 00:54:19 -04:00
8776b81033
add virial support to fix addforce
2017-09-15 00:46:18 -04:00
f1fce64ff9
Fix small typo to calculation of accumulated work in Colvars
2017-09-14 12:58:00 -04:00
da7776f818
Bugfix for the limit keyword
2017-09-14 11:00:55 +02:00
66f59f9ec0
FindLATTE.cmake: fixed a typo
2017-09-13 15:51:03 -06:00
d84825fd7f
remove useless files
2017-09-13 14:37:24 -06:00
f971cd6e45
Merge pull request #647 from rbberger/gpu_opencl_2
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Use OpenCL 2.x API in GPU package when supported
2017-09-12 10:56:13 -06:00
0cb3a3821f
Merge pull request #644 from akohlmey/collected-small-fixes
...
Collected small fixes for next patch
2017-09-12 10:31:51 -06:00
e927794696
Merge pull request #643 from andeplane/gpu_opencl_compile_fix
...
Fixed OpenCL compilation issues with __global keywords
2017-09-12 10:31:22 -06:00
e196a2b9e5
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
cb19ef547e
update src/.gitignore
2017-09-11 22:00:58 -04:00
95d8492853
the original fix qeq went away over 7 years ago, we don't need to purge it
2017-09-11 21:59:22 -04:00
b3547a9eca
add infrastructure for enabling fixes to contribute to the virial by aidan
2017-09-11 11:09:59 -04:00
84b84c10db
Use OpenCL 2.x API in GPU package when supported
2017-09-09 19:53:56 -04:00
0be7f46750
cmake: added USER-MESO
2017-09-09 08:25:57 -06:00
4738fedca3
Merge remote-tracking branch 'origin/master' into cmake_improvements
2017-09-09 08:22:30 -06:00
1601433ca1
cmake: fix lib suffix
2017-09-09 07:05:51 -06:00
3fdb6f10fa
cmake: OpenCL is always found if required
2017-09-09 06:51:24 -06:00
ff18cff46b
Merge branch 'cmake_pkg_libs' into cmake_improvements
2017-09-08 23:34:59 -04:00
8a06a7bc6b
Add OpenCL support to CMake build
2017-09-08 22:20:47 -04:00
bf9f084d72
update rigid fix styles in USER-OMP for changes in RIGID package
2017-09-08 14:09:44 -04:00
b861ea342e
cmake: fix LATTE linkage
2017-09-08 11:54:32 -06:00
fce633aa5f
cmake: tweaks for EXAALT superbuild, add latte_fix
2017-09-08 11:33:49 -06:00
2f6be88c4a
Merge remote-tracking branch 'origin/master' into exaalt
2017-09-08 07:04:12 -06:00
7b1542a0ba
merging stable and exaalt branches into exaaltstable
2017-09-07 16:31:50 -06:00
08bdc4e422
minor cleanup
2017-09-07 12:01:19 -04:00
eb0e64b2f3
must forward modify_param() processing to FixRigid base class
2017-09-07 12:00:33 -04:00
366d087027
update docs for changes to makefiles
2017-09-06 14:20:24 -04:00
3a5d8362ff
have only one common MPI makefile for KOKKOS with CUDA
2017-09-06 14:16:17 -04:00
5089b263b2
make kokkos_cuda_mpi compatible with both MPICH and OpenMPI
2017-09-06 14:15:27 -04:00
de8297ea19
recover ability to compile USER-INTEL without OpenMP enabled
2017-09-06 12:02:14 -04:00
fe557cb882
fix typo in commands table
2017-09-06 11:35:52 -04:00
c80203cb01
Merge pull request #641 from lammps/doc-tweak
...
small update to docs for new commands
2017-09-06 08:52:51 -06:00
4161868bcf
Merge pull request #640 from ohenrich/user-cgdna
...
USER-CGDNA - sequence-dependent stacking and h-bonding strength
2017-09-06 08:52:05 -06:00
9ca39c89a6
Merge pull request #639 from rbberger/python_interface_improvements
...
Python interface improvements
2017-09-06 08:51:27 -06:00
99791ce01c
Merge pull request #632 from timattox/USER-DPD_kokkos_merge
...
Add Kokkos version of the USER-DPD package
2017-09-06 08:50:43 -06:00
0248a7b98e
remove duplicate listing of deleted USER-DPD files from Purge.list
2017-09-06 09:24:05 -05:00
dbc60d949f
Fixed OpenCL compilation issues with __global keywords
2017-09-06 15:08:02 +02:00
fd0fae4847
Langevin thermostat applied only at post_force in rigid-body fixes
2017-09-05 23:40:14 -03:00
cccd6c441c
Conditional late computation added to rigid_nh and rigid_nh_small
2017-09-05 23:27:26 -03:00
d886cc91f3
fix syntax error in fix saed/vtk docs example
...
This addresses the issue reported on github
by @subhammridha closes thus clodes #642
2017-09-05 17:45:56 -04:00
4c5d901e2b
fix stupid typo (too much compiling of fortran codes...)
2017-09-05 16:45:03 -04:00
c8f92c1a61
add a couple deleted files from USER-DPD to Purge.list
2017-09-05 16:42:58 -04:00
dec1d7b2dc
re-indent so that gcc no longer complains about inconsistent indentation
2017-09-05 16:41:19 -04:00
45602e58f9
fix another couple of typos
2017-09-05 12:48:28 -04:00
cd72532fb9
fix typo
2017-09-05 12:47:34 -04:00
b170606052
Merge pull request #620 from amilumas/master
...
Temper_NPT
2017-09-05 10:08:55 -06:00
65b295e826
Merge pull request #638 from jdevemy/master
...
Mods for extra/special/per/atom and add toluene
2017-09-05 10:05:49 -06:00
89a0bc947f
small update to docs for new commands
2017-09-05 10:04:20 -06:00
c8967a335f
Included hyperlink to package
2017-09-05 11:45:32 +01:00
2105145f55
More minor changes
2017-09-05 11:40:36 +01:00
f7715ab6ce
Added comment about optimised damping coefficient for BD
2017-09-05 11:35:26 +01:00
12fe614ddf
Added sequence-dependent stacking and base-pairing strength
2017-09-05 10:48:38 +01:00
0b5a2e199d
Add way of getting correct ctypes integer type for bigint, tagint, and imageint
2017-09-04 20:01:31 -04:00
09bb687918
Correct indentation
2017-09-04 20:01:04 -04:00
bb3ee752e5
Added optional numpy access to atom data
...
The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.
To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
2017-09-04 19:59:50 -04:00
6b2d321d18
Add missing globals in library interface
2017-09-04 19:57:02 -04:00
88d54d49b8
Documentation entries for fix_modify bodyforces option
2017-09-01 17:40:49 -03:00
3d614bbc87
Bug fix in multiple fix rigid check
2017-09-01 12:23:48 -03:00
2b9646097c
Merge branch 'master' of github.com:lammps/lammps
2017-09-01 09:16:11 -06:00
f58088ae61
patch 1Sep17
2017-09-01 09:15:37 -06:00
6e945f72f4
Keyword 'bodyforces' added to fix_modify command
...
- Applies to classes FixRigid, FixRigidSmall, and FixPOEMS
2017-09-01 00:16:54 -03:00
251bc882cf
put back modify_params() API that was removed in error
2017-08-31 16:25:16 -04:00
f56a345ae9
implement "earlyflag" to select when to compute body torques/forces
2017-08-31 16:15:39 -04:00
76cc545d2a
convert early fix ordering error to warning
2017-08-31 16:14:45 -04:00
397bc225b2
add temper/npt to src/USER-MISC/README
2017-08-31 14:56:43 -04:00
d9d9ba8244
update .gitignore
2017-08-31 14:52:56 -04:00
eba4be18c2
adapt formatting and naming conventions to fully match LAMMPS style. allow rigid and accelerated integrators.
2017-08-31 14:48:30 -04:00
4d2ed30b35
add reference outputs to temper/npt example
2017-08-31 14:13:02 -04:00
f3dda30f8e
fully integrate temper/npt command into manual
2017-08-31 13:53:40 -04:00
d95a5f219e
Remove all thread fences except one in verlet_kokkos
2017-08-31 10:38:36 -06:00
a5b65c1af4
Mods for extra/special/per/atom and add toluene
2017-08-31 15:03:04 +02:00
3e6cdd1400
USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT
2017-08-30 14:58:38 -05:00
dc7f1281b8
USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet
...
The Constant Energy DPD (DPDE) was our primary usage case, so only stubs
for the Constant Temperature case were included in Kokkos code so far.
The non-Kokkos version works fine for Constant Temperature DPD.
2017-08-30 11:01:17 -05:00
27c962dc3b
link cuda in gpu only, remove duplicated incl. dir
2017-08-30 09:45:01 -06:00
2dd202cc76
USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp
2017-08-30 10:34:09 -05:00
f2d8c37f27
Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT
2017-08-30 10:24:29 -05:00
a4a45f1d9c
Remove unnecessary check in npair_kokkos
2017-08-29 17:25:13 -06:00
f57d194920
Add files via upload
...
documentation for temper/npt
2017-08-29 10:40:37 -04:00
34b3fc2157
Fix GPU CMake compilation
2017-08-29 01:20:34 -04:00
098861375b
SOVERSION not needed for STATIC libs
2017-08-28 16:18:58 -06:00
19b77857dc
fix Fortran flags for MEAM
2017-08-28 14:59:01 -06:00
bd9dc4886d
cmake: README is markdown
2017-08-28 14:27:12 -06:00
9207f6540e
fix liblammps install
2017-08-28 14:11:21 -06:00
736e063971
Merge branch 'master' ( 21893539cb Aug 25) into USER-DPD_kokkos_merge
...
Resolved conflicts in src/KOKKOS/npair_kokkos.cpp
2017-08-28 14:46:50 -05:00
62928a1637
make GPU flags local to libgpu
2017-08-28 13:24:41 -06:00
c8dfe0c3de
drop BUILD_SHARED_PKG_LIBS and make all pkglibs static
2017-08-28 13:17:27 -06:00
6a4bbddb3b
Add files via upload
...
data file for example
2017-08-28 14:56:37 -04:00
2add18e013
Create in.temper_npt
...
example for temper/npt
2017-08-28 14:55:43 -04:00
d0efd3a422
Add files via upload
...
Updated command to temper/npt instead of temper_npt
2017-08-28 14:48:00 -04:00
f47cc0aab5
simpilfy pkg lib build
2017-08-27 18:55:28 -06:00
57872c8b60
drop INSTALL_LIB option
2017-08-27 18:42:32 -06:00
4bff008777
enable PIC globally
2017-08-27 18:40:55 -06:00
eed4815953
Non-rigid fixes with post-force() not allowed after fix poems
2017-08-27 20:03:28 -03:00
fa5ec0bae7
Fixes with post-force() not allowed after fix rigid or rigid/small
2017-08-27 19:22:37 -03:00
153c771a6d
Use PIC in mpi_stubs when BUILD_SHARED_LIBS=on
2017-08-27 17:27:43 -04:00
313b8bc2fa
build lib/gpu as a library
2017-08-27 17:00:56 -04:00
5308ee67fa
fix shared build and mscg install
2017-08-27 13:45:48 -06:00
c196025ea9
make molfile less special
2017-08-27 12:23:30 -06:00
bc11868986
cmake: fixed a typo
2017-08-27 12:13:35 -06:00
e4415735f2
check for '-fno-second-underscore'
2017-08-27 12:10:46 -06:00
98f27162ba
make libmpi_stubs
2017-08-27 11:37:57 -06:00
bdc117bf10
cmake: convert mscg into a lib
2017-08-27 07:15:00 -06:00
b7ec720f91
link QUIP against LAPACK_LIB too
2017-08-27 07:13:55 -06:00
47f16c0d70
cmake: move shared libs install warning in one place
2017-08-27 07:06:08 -06:00
76926b7fcf
Compile linalg as library and track link dependencies for correct link order
2017-08-27 03:54:40 -04:00
67ae2719a8
Simplify lib build by using target_include_directories
2017-08-27 03:04:32 -04:00
7572dc63db
Computation of forces/torques on rigid bodies moved to post_force
2017-08-26 18:24:47 -03:00
21893539cb
Merge pull request #633 from lammps/doc-user-meso
...
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
2017-08-25 17:41:00 -06:00
dd101db79c
Merge pull request #582 from stanmoore1/kk_changes
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Fixing execution space issues in KOKKOS package
2017-08-25 17:06:26 -06:00
81ba181349
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
2017-08-25 17:04:36 -06:00
e52a28f8af
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
01dd0e173e
Merge branch 'master' into USER-DPD_kokkos_merge
2017-08-25 16:02:27 -06:00
1f8c4f2c62
Remove hardcoded map variables and debug output
2017-08-25 15:31:00 -06:00
b73999ef21
Revert change to read_data.cpp
2017-08-25 15:25:41 -06:00
1e16fed9ab
Error out if using pair hybrid with Kokkos, but not pair hybrid/overlay
2017-08-25 15:16:19 -06:00
a062944de9
Fix execution space issues
2017-08-25 14:45:47 -06:00
a641289d5b
Must use atomics for GPUs in pair_exp6_rx_kokkos
2017-08-25 12:36:53 -06:00
6195b3c0f6
Merge pull request #631 from akohlmey/small-fixes-and-updates
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Small fixes and updates for patch release
2017-08-24 08:35:32 -06:00
de0fdbed6c
moltemplate bugfix update
2017-08-24 07:12:45 -04:00
dea92fbf52
print write dump systen init warning only on MPI rank 0
2017-08-23 21:01:55 -04:00
6db3bd87ee
correct typo in header formatting
2017-08-23 17:52:09 -04:00
e55fa9d320
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
2017-08-23 15:21:39 -06:00
cbf3646806
Merge branch 'master' into USER-DPD_kokkos
2017-08-23 15:20:56 -06:00
f5a99dece7
Remove unnecessary thread fences
2017-08-23 15:08:44 -06:00
4784506ba9
Remove unused function in rand_pool_wrap_kokkos
2017-08-23 15:02:26 -06:00
270abff2a2
Fix compile error for CUDA in pair_exp6_rx_kokkos
2017-08-23 14:59:19 -06:00
b6c93f96cf
Merge pull request #629 from stanmoore1/kokkos_update
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Update Kokkos library to v2.04.00
2017-08-23 14:39:42 -06:00
7b7a5076d0
Merge pull request #624 from akohlmey/compute-fragment
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Add computes fragment/atom and aggregate/atom
2017-08-23 14:14:33 -06:00
1536eb5de5
Merge pull request #630 from akohlmey/moltemplate-update
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Update for moltemplate to version 2017-8-22
2017-08-23 14:13:07 -06:00
f7a0a6eb70
Merge pull request #622 from akohlmey/collected-small-fixes
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Collected small fixes
2017-08-23 14:12:45 -06:00
d80a6cbd31
Merge pull request #621 from lammps/user-meso
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new USER-MESO package
2017-08-23 14:12:18 -06:00
c4b37039ab
Merge pull request #619 from jrgissing/molecule_maxspecial
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molecule maxspecial value corrected when specials autogenerated
2017-08-23 14:11:47 -06:00
b52efa2850
add compatibility to NetCDF 4.3.3 as bundled with RHEL 7.x
2017-08-23 15:28:27 -04:00
e88ff8d6f9
correct embedded help for GPU lib Install.py
2017-08-23 15:20:30 -04:00
97edf90a73
update fix qeq docs for the new, more flexible parameter file format
2017-08-23 11:22:09 -04:00
12150ffa73
add moltemplate version 2017-8-22
2017-08-23 07:54:56 -04:00
57aafba7c3
remove old moltemplate version
2017-08-23 07:54:05 -04:00
cdfb1aa043
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
b80752a40c
restore changes to read_data docs, that would have been lost due to merging an outdated version
2017-08-23 00:01:19 -04:00
79d5ca669d
fix issues indicated by compiler warnings
2017-08-22 23:46:32 -04:00
26c15140be
add USER-MESO files to .gitignore
2017-08-22 23:46:09 -04:00
5c985946d5
Merge branch 'master' into USER-DPD_kokkos
2017-08-22 13:50:19 -06:00
090c792d90
Update Kokkos library to v2.04.00
2017-08-22 13:42:02 -06:00
c5ccbbeea7
cmake: fix 'make test'
2017-08-22 07:13:04 -06:00
e2a1b666be
Merge remote-tracking branch 'junghans/cmake_flags_summary' into cmake_improvements
2017-08-21 20:54:24 -04:00
ad0ecfa507
Merge remote-tracking branch 'junghans/lammps_suffix' into cmake_improvements
2017-08-21 20:53:53 -04:00
cf3f15b0a5
cmake: make h5md includes local
2017-08-21 15:04:03 -06:00
5fcc19777c
cmake: fix molfile compile
2017-08-21 14:24:00 -06:00
1f4c550f9f
cmake: make awpmd includes local
2017-08-21 13:09:52 -06:00
24c00b1f7a
fix typo
2017-08-21 13:12:48 -04:00
5a0c3aea8a
add a compute aggregate/atom, that combines the rules for compute cluster/atom and fragment/atom
2017-08-21 13:12:43 -04:00
c8aa06b959
cmake: build libs separate
2017-08-21 11:12:36 -06:00
bdccdbf2c2
cmake: make linker flags more clear
2017-08-21 10:20:56 -06:00
6d86697b3f
cmake: move option in user options block
2017-08-21 10:18:20 -06:00
d1a0c040c9
add initializers for nmatch/nwant variables in molecule file parser
2017-08-20 23:28:13 -04:00
892a3f8609
cmake: make _ in LAMMPS_MACHINE implicit
2017-08-20 09:39:51 -06:00
de5883b7bb
cmake: LAMMPS_SUFFIX -> LAMMPS_MACHINE
2017-08-20 09:27:12 -06:00
b1615d1839
cmake: print flag summary
2017-08-20 09:17:49 -06:00
aef2416ece
Simplify CMake script
2017-08-20 10:49:30 -04:00
00a78cfa1a
cmake: add LAMMPS_SUFFIX
2017-08-20 08:30:09 -06:00
f5b8f722ee
remove non-portable non-ascii blanks from fix wall/ees docs
2017-08-20 10:09:21 -04:00
39e51df2c0
add missing entry in pdf manual
2017-08-20 10:02:11 -04:00
c895df73d6
skip over disabled bonds
2017-08-20 09:49:01 -04:00
4dc1195cd8
add docs for compute fragment/atom
2017-08-20 09:41:49 -04:00
35fd82b602
trim unneeded includes
2017-08-20 09:19:04 -04:00
c5ce3ffe60
use list of bonds per atom instead of bondlist, as that will work with shake as well
2017-08-20 09:18:04 -04:00
c9d41dbb47
Ignore installed package files when using cmake
2017-08-19 06:33:27 -04:00
1a80d4bc13
Remove style files in src dir while running cmake
2017-08-19 05:55:51 -04:00
aa1ce09b12
more cleanup, checks and generalization of QEQ parameter file parsing
2017-08-18 20:03:47 -04:00
f945d4567d
new USER-MESO package
2017-08-18 17:33:42 -06:00
44ccdb86df
add checks when reading QEQ parameter file to avoid segfaults and memory corruption on incorrect files
2017-08-18 19:24:39 -04:00
2e6a928aa3
ignore file recently added to USER-INTEL
2017-08-18 19:23:33 -04:00
6f66e6c454
add new compute fragment/atom
2017-08-18 19:07:32 -04:00
822bffdfae
Merge pull request #1 from amilumas/temper_npt
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Temper_NPT and example
2017-08-18 15:29:59 -04:00
6aa756968d
Temper_NPT and example
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New function that allows for parallel tempering (replica exchange) in MD in LAMMPS in the isothermal-isobaric ensemble (NPT)
Similar to temper which works in the canonical (NVT) ensemble.
An example is included that uses temper_npt
2017-08-18 15:21:49 -04:00
d671a04274
whitespace cleanup
2017-08-18 14:24:09 -04:00
bf7cff73d4
allocate the temporary special array on the heap and not the stack (it may get too big quickly) and clear the array before use.
2017-08-18 14:23:48 -04:00
9e85b3178a
molecule maxspecial value corrected when specials autogenerated
2017-08-17 21:39:25 -06:00
b11fe2eddb
Merge pull request #573 from junghans/cmake
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Add secondary, cmake based build system
2017-08-17 16:06:19 -06:00
7ddcb6812b
patch 17Aug17
2017-08-17 16:02:20 -06:00
76cd61350d
Merge pull request #613 from akohlmey/collected-small-changes
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Collected small changes and bug fixes
2017-08-17 11:34:52 -06:00
fa3c0c61d6
Merge pull request #618 from lammps/intel
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USER-INTEL add-ons from Mike
2017-08-17 11:32:53 -06:00
c46d5ff422
Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10
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Minor fixes to Colvars module
2017-08-17 11:32:38 -06:00
dd67989c76
Merge pull request #601 from stanmoore1/kokkos_update
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Update Kokkos library to v2.03.13
2017-08-17 11:32:18 -06:00
00aafef1a8
Merge pull request #597 from ndtrung81/three-body-short-nlist
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Implementing short neighbor lists for three-body gpu styles
2017-08-17 11:31:59 -06:00
7175abcc71
flag more pair styles as supporting USER-INTEL to match newly added code
2017-08-16 13:58:46 -04:00
e34b20405c
Fix a couple of typos in the docs
2017-08-15 21:10:05 -04:00
1d4d2155a2
USER-INTEL add-ons from Mike
2017-08-15 17:12:07 -06:00
cee87d7a54
update manual to point to packages.lammps.org instead of rpm.lammps.org
2017-08-15 16:19:09 -04:00
60e14f1490
add comment to msi2lmp README about symmetry limitations
2017-08-14 08:54:26 -04:00
81e7d4a942
fix incorrect preprocessor define for windows
2017-08-12 00:35:50 -04:00
13b804eeeb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 10Aug17
2017-08-11 14:53:44 -04:00
4041db8d1a
Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17
2017-08-11 13:25:28 -04:00
8c16ea1bfc
add automatic triggering of review requests with a code owners file
2017-08-10 15:58:51 -04:00
c8741f3a01
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
2a7d2dee36
add more strict checking of data when parsing molecule files to detect format errors
2017-08-10 14:49:51 -04:00
378989e065
Merge pull request #27 from timattox/USER-DPD_kokkos_update
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Merge changes thru July 27, 2017 from master 6d0a228667a0183b7f9a331c
2017-08-10 13:21:53 -04:00
da01be7c18
More robust change from initial to target restraint centers in Colvars
2017-08-10 09:22:53 -04:00
e86b139817
Merge pull request #25 from timattox/USER-DPD_GBhacks_cudafix
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Fix CUDA runtime issues for USER-DPD Kokkos code.
2017-08-09 15:32:03 -04:00
3e9b41c6b7
Added references to GPU package citations
2017-08-09 10:09:40 -05:00
8a7a831bd6
Remove redundant check in Makefile.kokkos
2017-08-08 12:57:22 -06:00
5cd1dc93dc
Revert 7edb294b44 temporarily
2017-07-31 15:32:20 -06:00
93190a548a
Merge branch 'cmake' of github.com:junghans/lammps into cmake
2017-07-31 11:48:27 -06:00
72f50c91ee
Add -DLAMMPS_EXCEPTIONS flag
2017-07-31 11:48:22 -06:00
408d9d99a9
cmake: improve some error messages
2017-07-31 11:35:41 -06:00
8431ca5fec
Remove tpls directory
2017-07-31 10:54:07 -06:00
13f2d39f55
Update Kokkos library to v2.03.13
2017-07-31 10:34:21 -06:00
7edb294b44
Fix execution space issues in comm_kokkos
2017-07-28 10:44:08 -06:00
9695aa6092
Merge branch 'master' into USER-DPD_kokkos_testing
2017-07-27 15:51:56 -06:00
8e834d8be1
Add missing sync to neigh_bond_kokkos
2017-07-27 09:37:16 -06:00
8f59c0e188
Fix modify/sync issue in neigh_bond_kokkos
2017-07-27 08:51:17 -06:00
0231cc38a3
cmake: some more typo fixes
2017-07-25 19:09:20 -06:00
c3c9f357fd
Fix concurrent modification issue in comm_kokkos
2017-07-25 14:37:41 -06:00
76fb4e0815
Merge branch 'master' into kk_changes
2017-07-25 14:16:31 -06:00
d3fa882280
Fix execution space issues in Kokkos EAM pairstyles
2017-07-25 13:49:23 -06:00
557e5b964a
Fixing Kokkos execution space issue with regions
2017-07-25 13:37:01 -06:00
633ca33f2f
Fix issue in Kokkos neighborlist
2017-07-25 13:08:24 -06:00
bc446bb8b0
Merge branch 'master' into USER-DPD_kokkos_testing
2017-07-25 12:12:30 -06:00
6716de5320
allow user to override PYTHON_INSTDIR
2017-07-24 20:17:17 -06:00
f2023431f6
cmake: fixed another typo
2017-07-24 12:54:26 -06:00
aa60ef6ed8
Cleaned up 3-body kernels, reverted some mistaken changes to vashishta
2017-07-23 00:08:55 -05:00
a71f5a0c20
Enabled again neigh no with tpa > 1 for 3-body gpu styles for backward compatibility, could be slower than neigh no tpa 1 in many cases
2017-07-22 22:57:37 -05:00
126d9cd3bc
add GZIP and FFMPEG status
2017-07-22 13:57:15 -06:00
8d485ea128
Remove hardcoded execution spaces
2017-07-21 16:04:18 -06:00
f4b6b67f6e
Fixing more execution space issues in KOKKOS package
2017-07-21 15:04:14 -06:00
8ed881947f
Fix execution space in manybody potentials
2017-07-21 14:28:13 -06:00
74deeeca58
cmake: fixed another typo
2017-07-21 11:50:13 -06:00
c010edc4fd
cmake: fixed two typos
2017-07-21 11:38:02 -06:00
3d1d0c58c7
Cleaned up 3-body gpu styles, and fixed a bug for tersoff/zbl/gpu.
...
There is a unresolved bug for neigh no with tpa > 1 with BaseThree, enforce tpa = 1 for neigh no in BaseThree for now.
2017-07-21 12:08:04 -05:00
e8e9ea8392
added one trivial test
2017-07-20 16:14:02 -06:00
c88d1e5510
make ENABLE_ALL work out of the box
2017-07-20 15:15:29 -06:00
427ca88dd4
cmake: error for POEMS + BODY package
2017-07-20 15:02:41 -06:00
1749d643c7
GPU: bring back CUDPP_OPT
2017-07-20 14:30:52 -06:00
f037f89f5f
fix GPU + BUILD_SHARED_LIBS
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X-Thanks: Robert Maynard <robert.maynard@kitware.com >
2017-07-20 14:12:23 -06:00
488609a5fd
make FFT a selective option
2017-07-19 18:54:15 -06:00
01bcb79bdc
cmake: clean up and updated comments
2017-07-19 18:34:07 -06:00
babba1870e
added FFTW2 support
2017-07-19 15:33:02 -06:00
a99e3ef4f0
cmake: fix typo and pkg info
2017-07-19 15:15:59 -06:00
c95db97b83
fix PYTHON install
2017-07-19 15:15:24 -06:00
2961ba7ebb
added MKL support
2017-07-19 10:35:48 -06:00
e2ad4fa745
GPU: cubin not needed
2017-07-18 19:29:40 -06:00
acbc60319f
GPU: clean up part 2
2017-07-18 18:43:51 -06:00
e6f5f77edf
GPU: clean up
2017-07-18 18:38:36 -06:00
864fd9cd87
remove cubin_headers hack
2017-07-18 18:20:23 -06:00
4d65c327f5
added minimal README
2017-07-18 16:06:29 -06:00
c3d9786616
GPU compiles
2017-07-18 16:01:35 -06:00
a9eaeb4d95
working on GPU build
2017-07-18 13:47:03 -06:00
1b34bec81a
Prefer DeviceType specification over RangePolicy
2017-07-18 10:59:34 -06:00
9df61b642e
Removing stray file
2017-07-18 10:44:45 -06:00
3c88b2a980
Fixing execution space issues in KOKKOS package
2017-07-18 09:53:26 -06:00
3c3baf34c4
GPU: added cuda includedir
2017-07-17 15:04:07 -06:00
8bc3184611
added support for LAMMPS_FFMPEG
2017-07-17 14:01:05 -06:00
050a82af58
fix LAMMPS_LONGLONG_TO_LONG description
2017-07-17 13:28:34 -06:00
99f5f82b02
added support for LAMMPS_MEMALIGN and LAMMPS_LONGLONG_TO_LONG
2017-07-17 13:26:46 -06:00
a3885b78ad
added support -DLAMMPS_XDR and -DPACK_*
2017-07-17 13:21:42 -06:00
08c920029f
added lammps size option
2017-07-17 12:22:28 -06:00
2411192ab4
cmake: add cross-configure warning
2017-07-17 11:52:06 -06:00
5ee2c31038
split PACKAGES, get ENABLE-ALL right
2017-07-17 11:01:08 -06:00
1c1a1db366
Fix typo
2017-07-17 11:55:05 -04:00
80e4448614
added GPU
2017-07-16 23:03:11 -06:00
385c6f7f2b
cmake: clean up
2017-07-16 22:53:53 -06:00
fc1be074b2
added USER-INTEL
2017-07-16 22:52:59 -06:00
7605f72c9a
finish USER-QMMM
2017-07-16 22:37:51 -06:00
22ecd9b8d2
started on USER-QMMM
2017-07-16 22:07:21 -06:00
7dd5068740
allow internal lapack
2017-07-16 21:43:29 -06:00
fa0f8a9e2a
added USER-QUIP
2017-07-16 21:31:57 -06:00
d6f05ea309
USER_OMP -> USER-OMP
2017-07-16 20:19:20 -06:00
b6385d6ce2
add OpenKIM support
2017-07-16 20:17:41 -06:00
2978cce8db
Added OPT
2017-07-16 20:52:38 -04:00
9991f679ae
added USER-VTK
2017-07-16 20:41:42 -04:00
fc2e8b3c5e
more USER packages
2017-07-16 17:52:43 -06:00
bb87bd4ac7
enable more user packages
2017-07-16 17:01:28 -06:00
d50b62837b
add USER-AWPMD
2017-07-16 16:45:28 -06:00
c64424754d
added USER-ATC
2017-07-16 16:18:58 -06:00
c549a16a85
enable REPLICA RIGID SHOCK SNAP SRD VORONOI
2017-07-16 11:30:09 -06:00
140182fb0b
added support for QEQ
2017-07-16 11:14:08 -06:00
742eee1966
added support for POEMS
2017-07-16 11:07:36 -06:00
4812d4c659
enable PERI
2017-07-16 10:48:29 -06:00
95d9d32307
add support for MSCG
2017-07-16 10:37:24 -06:00
f50a757dc6
added MPIIO support
2017-07-16 08:32:14 -06:00
01f5136584
cmake: clean up
2017-07-16 08:22:19 -06:00
fa1f38596c
Add support for PYTHON in CMake build
2017-07-15 18:29:33 -05:00
23540cfc94
enable MISC
2017-07-15 16:54:27 -06:00
fdb5ccefc7
Merge branch 'cmake' of github.com:junghans/lammps into cmake
2017-07-15 17:47:53 -05:00
629f112915
add support for MEAM
2017-07-15 16:44:03 -06:00
acd315e97a
Add basic KOKKOS support to CMake build
2017-07-15 15:33:36 -05:00
b15f75d37b
Merge branch 'cmake' of github.com:junghans/lammps into cmake
2017-07-14 22:08:06 -05:00
5e841bfe15
Added USER-OMP support to CMake build
2017-07-14 22:07:53 -05:00
d079b2f758
CreateStyleHeader: use temp file
2017-07-14 18:37:06 -06:00
54f2b02ac8
cmake: fix install
2017-07-14 18:33:27 -06:00
0a6e9c8bf6
added ENABLE_ALL option
2017-07-14 17:41:13 -06:00
b85979503f
Add CMake support for more packages
...
BODY, COLLOID, CLASS2, COMPRESS, CORESHELL, DIPOLE, GRANULAR, MC, MOLECULE, MANYBODY, RIGID
2017-07-14 18:19:59 -05:00
c7e218f310
Merge branch 'cmake' of github.com:junghans/lammps into cmake
2017-07-14 18:06:27 -05:00
335ef11a7b
Added style header generation with CMake
2017-07-14 17:49:05 -05:00
d5dcb3d329
add support for KSPACE
2017-07-14 15:55:36 -06:00
c07adac22d
add support for LAMMPS_GZIP
2017-07-14 14:49:53 -06:00
e4e1252152
fix LAMMPS_PNG
2017-07-14 14:44:44 -06:00
842dc1b58c
cmake: collect link libs
2017-07-14 14:21:21 -06:00
60faca2896
added tilt factors
2017-07-14 10:05:38 -06:00
a566419ca6
Add LAMMPS_LIB_SOURCE_DIR variable in CMakeLists.txt
2017-07-14 04:36:52 -05:00
fdd3d802f0
Clean up CMakeList.txt by introducing LAMMPS_SOURCE_DIR variable
2017-07-14 04:00:38 -05:00
a86b0d4c1b
Add PNG library detection to CMakeList.txt
2017-07-14 03:53:07 -05:00
7f1789a0c4
cmake: add support for REAX and hence Fortran
2017-07-13 23:30:46 -06:00
bfb449cec9
cmake: furhter improvments
...
* Add support for one package
* Add support for JPEG as external package
* Use pre-generated style header
* TODO write a script to generate them
2017-07-13 22:54:51 -06:00
6b19016deb
cmake: initial commit
2017-07-12 16:23:38 -06:00
cdac5f496c
Built 3-body short neighbor list for the 3-body kernels using per-pair cutoffs for vashishta gpu style
2017-07-11 00:13:56 -05:00
8c9db3ea00
Built 2-body short neighbor list and used for 2-body kernels in tersoff gpu styles
2017-07-10 23:50:21 -05:00
ea2b01e83b
Refactored 3-body gpu styles to remove code duplication
2017-07-08 20:17:31 -05:00
34fe2273f6
Added short neighbor list implementation for tersoff/zbl/gpu and tersoff/mod/gpu
2017-07-08 14:59:48 -05:00
77c60189b8
Minor cleanups for tersoff/gpu
2017-07-08 14:43:53 -05:00
1c6533e53d
Working on short neighbor list for tersoff/gpu
2017-07-08 14:15:26 -05:00
68206079da
Supported short neighbor lists for 3-body kernels in sw/gpu and vashishta/gpu
2017-07-07 16:47:24 -05:00
ea4d11fc5e
Merge branch 'master' into USER-DPD_kokkos_testing
2017-06-26 09:36:30 -06:00
67a0183b33
Removing atom2bin change since ssa neighlists aren't be used for occasional lists
2017-06-19 15:23:33 -06:00
b96b6b9cd7
Fixing error checks
2017-06-19 14:04:16 -06:00
da0dcbe0bb
Updating to master
2017-06-19 10:56:24 -06:00
3c8e75ad59
Add missing sync/modify to fix_shardlow_kokkos
2017-06-09 10:57:35 -06:00
c51cadcc6c
Fixing CUDA runtime issues in fix_shardlow_kokkos
2017-06-09 09:31:37 -06:00
86497949f2
Fixing CUDA runtime issues in fix_shardlow_kokkos
2017-06-08 13:40:20 -06:00
b4b7310884
Fixing CUDA runtime issues in pair_exp6_rx_kokkos
2017-06-08 13:33:23 -06:00
046900cd51
Merge pull request #26 from timattox/USER-DPD_GBhacks_optimize
...
Reduce memory churn in several files
2017-06-08 10:50:36 -06:00
43cfa10ea4
Reduce memory churn in pair_multi_lucy_rx_kokkos
2017-06-08 09:58:10 -06:00
6f24c58c1a
Reduce memory churn in fix_rx_kokkos
2017-06-08 09:52:00 -06:00
611bb6f130
Reduce memory churn in pair_table_rx_kokkos
2017-06-08 09:31:51 -06:00
520ab26bd9
Fixing more CUDA runtime issues
2017-06-07 15:07:53 -06:00
efe60bf991
Fixing more CUDA runtime issues
2017-06-06 13:10:04 -06:00
36cbe43978
Fixing some CUDA runtime issues in npair_ssa_kokkos
2017-06-06 10:51:26 -06:00
2cf83d9fca
Updating from master to 19May17
2017-05-25 11:21:10 -06:00
6032b8846e
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
2017-05-17 11:36:50 -06:00
98713680ec
added alternative linking line for intel mkl
2017-05-17 11:36:31 -06:00
ca4619e227
Fix format issue in pair_exp6_rx_kokkos
2017-04-11 09:14:21 -06:00
6c0b691882
Removing more memory churn in pair_exp6_rx_kokkos
2017-04-11 09:12:46 -06:00
035d0a80d7
Reducing memory churn in pair_exp6_rx_kokkos
2017-04-10 16:38:58 -06:00
178af2ec9e
USER-DPD Kokkos: use a parallel_for() to build the ghosts workplan for SSA
2017-04-06 03:53:57 -04:00
9e272cb393
USER-DPD Kokkos: use a parallel_for() to build the locals workplan for SSA
2017-04-06 02:31:45 -04:00
ad5481831f
Merge branch 'USER-DPD_GBhacks' into USER-DPD_GBhacks_ssa_mem as of patch 31March17
2017-04-05 16:38:44 -04:00
456926a321
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 31March17
2017-04-05 16:18:39 -04:00
bceaa57614
Merge branch 'master' into USER-DPD_kokkos as of patch 31Mar17
2017-04-05 15:05:47 -04:00
4d4b6f66b7
Changing default gb/test to on
2017-04-05 11:42:25 -06:00
aedd7c57f3
Reset atom map values from restart file
2017-04-03 16:42:18 -06:00
2b2f3bd57c
USER-DPD Kokkos: #ifdef DEBUG_SSA_BUILD_LOCALS the new debug output
2017-04-02 00:07:24 -04:00
c4c3d490c7
USER-DPD Kokkos: preflight storage needed for SSA threaded neigh list build
2017-04-01 23:52:14 -04:00
e0021a3ff5
USER-DPD Kokkos: preflight SSA neigh list workplan to reduce allocated storage
2017-04-01 14:41:52 -04:00
ac4c35ce8d
USER-DPD Kokkos: more WIP on preflighting SSA neighbor list build, with debugging
2017-04-01 13:45:29 -04:00
ac64183ecf
USER-DPD Kokkos: WIP on preflighting SSA neighbor list build, with debugging
2017-04-01 12:11:55 -04:00
6ba59cb458
fix memory leak in fix_shardlow_kokkos
2017-03-31 17:04:39 -06:00
fe82926c1f
fix memory leaks in pair_tabl_rx_kokkos
2017-03-31 17:04:27 -06:00
697b072552
Merge pull request #21 from ibaned/dpd-memleaks
...
DPD memory leaks: round 2
2017-03-31 16:43:25 -06:00
5edbd63920
fix memory leak in fix_shardlow_kokkos
2017-03-31 16:03:05 -06:00
bf4f0817d4
fix memory leaks in pair_tabl_rx_kokkos
2017-03-31 15:57:00 -06:00
085958f065
Merge remote-tracking branch 'timattox/USER-DPD_GBhacks' into dpd-memleaks
2017-03-31 15:02:02 -06:00
b3d6d9f8cf
fix memory leak via NeighListKokkos::clean_copy()
...
There were several clean_copy() calls in pair
styles *outside device code*.
They seem to have been left over from an abandoned
effort to copy the Kokkos neighbor list as
a member of the pair style, instead of copying
out the individual views needed.
These leftover clean_copy() calls were setting
pointers to NULL that had not been freed,
leading to large memory leaks.
I've removed the clean_copy() function entirely,
and replaced it with the copymode flag system used
in many other Kokkos objects.
The copymode flag is only set to one in
functors that hold copies of the neighbor list.
2017-03-28 13:01:22 -06:00
7041f75fce
Merge pull request #20 from ibaned/dpd-memleaks
...
fix memory leak via NeighListKokkos::clean_copy()
2017-03-28 12:53:34 -06:00
20ae05055d
fix memory leak via NeighListKokkos::clean_copy()
...
There were several clean_copy() calls in pair
styles *outside device code*.
They seem to have been left over from an abandoned
effort to copy the Kokkos neighbor list as
a member of the pair style, instead of copying
out the individual views needed.
These leftover clean_copy() calls were setting
pointers to NULL that had not been freed,
leading to large memory leaks.
I've removed the clean_copy() function entirely,
and replaced it with the copymode flag system used
in many other Kokkos objects.
The copymode flag is only set to one in
functors that hold copies of the neighbor list.
2017-03-28 11:38:26 -06:00
661bd37e15
Make read_restart evenly divide the work of reading when using mpiio.
...
Currently only affects restart files written without any per-atom fix data.
2017-03-27 15:03:34 -05:00
0463923e33
USER-DPD Kokkos: tighten up the SSA data allocation to what is needed.
...
A future version was planned to use more space for a ghost work queue.
2017-03-27 11:04:41 -05:00
28784a4ce2
Now with the correct math, make read_restart properly size the atom_vec_* data
2017-03-27 08:38:40 -05:00
5f0823172c
Make read_restart properly size the atom_vec_* data when reading via mpiio
2017-03-27 06:56:28 -04:00
b418b46a03
USER-DPD: bugfix for an array that changed length in the non-kokkos version.
2017-03-27 06:56:16 -04:00
df95b2c566
testing simple ci, more complex #1
2017-03-23 22:27:42 -06:00
969325bf44
testing simple ci, attempt 4
2017-03-23 10:08:09 -06:00
e598762857
testing simple ci, attempt 3
2017-03-23 10:04:03 -06:00
8d793d4223
testing simple ci, attempt 2
2017-03-23 10:03:24 -06:00
756c899564
testing simple ci
2017-03-23 10:01:21 -06:00
3533df38d8
Merge branch 'virial1' into 'exaalt'
...
cleaned fix latte
See merge request !1
2017-03-22 15:48:36 +00:00
f7bdf128ea
cleaned fix latte
2017-03-22 09:35:47 -06:00
7ed500e829
added virial
2017-03-21 17:09:42 -06:00
3c91f9734d
make RK solver check in fix_rx_kokkos.cpp be as lenient as in fix_rx.cpp
...
NOTE: the (y < -MY_EPSILON) test was too strict, but don't know by how much
This needs to be revisited before merging back to LAMMPS master.
2017-03-21 17:12:09 -04:00
4ad1c82fcf
Merge branch 'USER-DPD_GBhacks' into USER-DPD_GBhacks_cps
2017-03-20 14:37:32 -04:00
ce94d7a4df
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
2017-03-20 12:16:01 -06:00
2c93065786
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-20 12:13:35 -06:00
20de98e898
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bring in bugfix
2017-03-19 21:22:59 -04:00
a68f3a93e5
USER-DPD Kokkos: bugfix, add a misisng line of code in pair_exp6_rx_kokkos.cpp
2017-03-19 21:12:52 -04:00
b3c46b7269
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bugfix for bonds
2017-03-17 20:15:24 -04:00
fff43a4604
USER-DPD Kokkos: bugfix for npair_ssa_kokkos.cpp corresponding to 0cd3f0cd
2017-03-17 19:33:04 -04:00
0cd3f0cd63
USER-DPD: bugfix for npair_half_bin_newton_ssa when bonds are involved.
...
Only locals have valid special[] arrays, so when finding neighbors of
ghosts, we have to swap the arguments to find_special().
2017-03-17 19:22:02 -04:00
75670244bb
Added ONE-TYPE template capability to vectorized_operator and cleaned up timers.
2017-03-17 17:02:47 -04:00
64fdb1f528
Kokkos/pair_exp6_rx_kokkos optimized for SIMD on the inner j-loop.
2017-03-17 15:52:40 -04:00
eb1a4d11dd
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, as of patch 17March17
2017-03-17 15:18:24 -04:00
1c749d5cf5
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-17 12:09:25 -06:00
a719f41426
Merge remote-tracking branch 'thunder/USER-DPD_kokkos_gb_test' into USER-DPD_GBhacks_cps
2017-03-17 10:26:44 -04:00
ba069fb755
Merge remote-tracking branch 'thunder/USER-DPD_GBhacks' into USER-DPD_GBhacks_cps
2017-03-17 10:11:00 -04:00
4a7bc115cb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bring in MPI deadlock fix
2017-03-17 03:24:03 -04:00
5ea096d08c
Merge branch 'master_bugfix_irregular' into USER-DPD_kokkos
2017-03-17 03:19:29 -04:00
ec192a95cb
Cleaned up the non-kokkos part of KOKKOS/pair_exp6_rx_kokkos.cpp
2017-03-16 22:28:19 -04:00
f5b7361ef6
Non-kokkos candidate of PairExp6rxKokkos::getMixingWeights to improve vectorization on the KNL.
...
- Moved the particle loop inside a replica of getMixingWeights, getMixingWeightsVect,
and refactored to improve vectorization.
- Added OMP SIMD and OMP threading directly inside that function but will replace with
kokkos parallel_for and parallel_reduce methods later.
2017-03-16 21:31:30 -04:00
acdb932c4e
Fixing index issue in pair_exp6_rx_kokkos
2017-03-16 09:28:27 -06:00
ce9b3f4fcb
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
2017-03-15 18:17:39 -05:00
7ebed717de
Adding gb_test
2017-03-15 16:05:51 -06:00
bdee2fa234
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-15 15:59:55 -06:00
bd7f4143e2
Merge pull request #18 from ibaned/pair-table-rx-kokkos-slow
...
pass Views by reference for pair_table_rx_kokkos
2017-03-15 09:47:42 -06:00
f4a08ba4fc
pass Views by reference for pair_table_rx_kokkos
...
this greatly speeds up pair_table_rx_kokkos,
and should put it on par with pair_table_rx
in the Serial case
2017-03-15 09:25:16 -06:00
5925460a27
Improve the performance of read_data of gzip'ed files using taskset.
...
Normally, the gzip process would be pinned to the same core as the
MPI rank 0 process, which makes the pipe stay in one core's cache,
but forces the two process to fight for that core, slowing things down.
2017-03-14 14:27:23 -05:00
d2cbfef13b
Add CUDA support to atom_vec_hybrid_kokkos
2017-03-13 09:01:35 -06:00
4b4bc7dc3b
USER-DPD: specialize PairTableRXKokkos's compute_all_items() on NEWTON_PAIR
...
No noticable performance change, but it does eliminate a deep conditional.
2017-03-13 03:03:27 -04:00
d5eceebf32
USER-DPD Kokkos: add support for full neighbor lists.
...
Note: "newton on" still required if using non-kokkos pair styles or fixes.
Non-kokkos pairs/fixes don't expect their half lists with newton off,
which happens if newton is turned off globally by kokkos via commandline.
Note2: Regardless, fix_shardlow* will still use half lists and newton on.
2017-03-13 01:56:00 -04:00
b1b377cb59
USER-DPD: fix_shardlow's neighbor request needs "newton on" override.
...
Even if other stuff is doing newton off, SSA must have it turned on.
2017-03-12 17:48:51 -04:00
e908b8dbea
USER-DPD Kokkos: correct some error messages
2017-03-12 16:20:09 -04:00
d6f6c6faf1
USER-DPD: Make newton-off warning in pair_dpd_fdt* be more selective.
...
If using fix_shardlow, the pair_dpd_fdt* styles are okay with newton off,
because the stocastic forces are thus only done in fix_shardlow.
2017-03-12 16:05:28 -04:00
17c8e695a4
Merge branch 'master' into USER-DPD_kokkos as of patch 10 Mar 2017
2017-03-10 21:37:52 -05:00
c7eadfdefd
Merge branch 'master' into USER-DPD_kokkos
2017-03-10 16:29:09 -05:00
6f71275db3
Add Kokkos version of atom_vec_hybrid_kokkos, without CUDA support
2017-03-09 15:35:07 -07:00
3298c37982
Makefile.lammps.gfortran for latte
2017-03-09 14:30:21 -07:00
35e1cf1d6e
Fixing issue with ev_setup in pair_hybrid_kokkos
2017-03-08 20:02:02 -07:00
fc23f9cfe8
Disable allocation of per-atom arrays in ev_setup for USER-DPD Kokkos styles
2017-03-08 13:07:52 -07:00
0ce5dc0234
Merge remote branch 'stanmoore1/ev_setup_kk' into USER-DPD_kokkos_ev_setup_bugfix
2017-03-08 13:05:15 -07:00
d01f09dce2
Turn off use of OpenMP in MPIIO/dump_custom_mpiio.cpp if Kokkos is in use.
...
The convert_string_omp() method breaks when Kokkos is also using OpenMP.
2017-03-07 15:23:17 -05:00
de27305227
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2017-03-07 11:47:18 -07:00
5b3101cb34
Merge pull request #16 from ibaned/cuda-runtime
...
Many CUDA runtime fixes
2017-03-06 16:02:52 -07:00
b8c72c7bdb
don't query device variables from the host
2017-03-06 15:51:09 -07:00
527a573026
don't use device views to measure dimensions
2017-03-06 15:42:26 -07:00
3e3a24da48
consolidate sorting functions
...
two sort functions with different
names but identical functionality.
making them the same function
until we descide to use a different
algorithm for atoms and ghosts
2017-03-06 15:28:25 -07:00
a7d1b571be
don't capture "this" in lambdas
...
CUDA lambdas can't capture the calling
object very well.
make local shallow copies of variables needed.
2017-03-06 15:07:07 -07:00
4a6f27935d
fix lambda syntax for CUDA
...
KOKKOS_LAMBDA doesn't quite work on CUDA,
you have to use LAMMPS_LAMBDA.
Also, if you do use LAMMPS_LAMBDA, you need
to run on the default device type,
i.e. no using lambdas to run on OpenMP
when LAMMPS has been compiled for CUDA.
2017-03-06 14:58:40 -07:00
a2c80d2cca
Merge remote-tracking branch 'fork/cuda-compile' into cuda-runtime
2017-03-06 14:50:43 -07:00
886cc69dfb
Merge pull request #15 from ibaned/cuda-compile
...
add missing KOKKOS_INLINE_FUNCTION to fix_shardlow
2017-03-06 11:05:49 -07:00
3e8cfb8247
The wonders of git commit -a
2017-03-06 11:04:47 -07:00
c2c22fc2ed
add missing KOKKOS_INLINE_FUNCTION to fix_shardlow
2017-03-06 10:57:19 -07:00
b35895ca12
USER-DPD Kokkos: Remove the SSA's ALLOW_NON_DETERMINISTIC_DPD option.
...
There was no measurable performance benefit to turning it on.
2017-03-03 15:21:09 -05:00
635c448b61
USER-DPD: sort bins for deterministic SSA instead of using Kokkos::Serial
2017-03-03 14:57:35 -05:00
c1739cae97
Merge pull request #14 from timattox/USER-DPD_kokkos_ssa
...
USER-DPD Kokkos: work around CUDA not having max_hardware_threads()
2017-03-03 13:29:20 -05:00
0651ea7f69
USER-DPD Kokkos: work around CUDA not having max_hardware_threads()
2017-03-03 12:50:13 -05:00
c468727db0
Fixing issue in fix_wall_lj93_kokkos
2017-03-03 10:49:15 -07:00
a7e8550962
USER-DPD Kokkos: turn one_type optimization into a template specialization
2017-03-03 10:38:45 -05:00
7e78921c96
USER-DPD Kokkos: propagate 763a00e8 bugfix to pair_multi_lucy_rx_kokkos.cpp
2017-03-03 10:12:44 -05:00
27d6284ebe
Merge branch 'USER-DPD_bugfix' into USER-DPD_kokkos, pair_multi_lucy_rx
2017-03-03 09:52:42 -05:00
f11b83ecd2
Merge branch 'USER-DPD_kokkos_ssa' into USER-DPD_kokkos
2017-03-02 16:37:03 -05:00
3820c5881d
Adding fix_wall_lj93_kokkos
2017-03-02 14:02:49 -07:00
27d2e9bf56
USER-DPD: add npair_halffull_newton_ssa to Purge.list
...
With the new SSA neighbor list, half from full can't work,
and will break compiles if the old files are in the src directory
2017-03-02 15:03:33 -05:00
d95fbf3a5e
USER-DPD Kokkos: use Random_XorShift64() by default, but allow overrides
2017-03-02 15:01:41 -05:00
5c6b0cc85c
removed fix_latte from src folder
2017-03-01 16:34:20 -07:00
03c05537fb
Merge branch 'USER-DPD_kokkos' into USER-DPD_kokkos_ssa_debug
2017-03-01 15:49:12 -05:00
8210b25fb8
USER-DPD Kokkos: replicate 9a560b90 bugfix to atom_vec_dpd_kokkos.cpp
2017-03-01 15:34:24 -05:00
8c625a52de
Merge branch 'USER-DPD_bugfix' into USER-DPD_kokkos, AtomVecDPD hybrid bugfix
2017-03-01 15:29:44 -05:00
ed089c34cf
USER-DPD Kokkos: Now use the deterministic Random_XorShift64() for SSA
2017-03-01 14:18:14 -05:00
268e855a15
USER-DPD Kokkos: bugfix for the rare case were the SSA ghost
...
processing has more parallelism than for the locals.
2017-03-01 14:14:29 -05:00
48ed963fd2
latte in added
2017-03-01 12:05:00 -07:00
1025c25548
latte.in added
2017-03-01 09:55:33 -07:00
78a8f75a8f
params added
2017-03-01 09:53:50 -07:00
641bf72f20
lib kokkos: Enable deterministic use of Random_XorShift*_Pool.
...
Add support for lock-free and deterministic use of Random_XorShift*_Pool
by giving state_idx selection and lock responsibility up to the
application. Done by an overload of get_state() to take sate_idx as
an argument that the appplication guarantees is concurrently unique
and within the range of num_states that the application passed to init().
In other words, this allows the RNG state to be associated with some
application specific index, rather than a runtime arbitrary thread ID,
and thus the application can control which work is performed using
which RNG in a deterministic manner, regardless of which thread
performs the work.
2017-03-01 11:52:33 -05:00
6e26358ec3
lib kokkos bugfix: on a CUDA host, the random state wasn't preserved.
...
Random_XorShift*_Pool<Kokkos::Cuda>::free_state() has two purposes:
1) update the state value kept in the pool
2) unlock the state
For a CUDA host thread, ONLY skip step 2, not both.
2017-03-01 11:46:26 -05:00
bf1794f59a
Merge branch 'USER-DPD_kokkos' into USER-DPD_kokkos_ssa_debug
2017-03-01 10:29:33 -05:00
0982331c71
USER-DPD Kokkos: replicate 7a593c2f bugfix to pair_table_rx_kokkos.cpp
2017-03-01 09:49:24 -05:00
3ae77e718a
Merge branch 'USER-DPD_bugfix' into USER-DPD_kokkos
2017-03-01 09:45:50 -05:00
b26a434a50
USER-DPD Kokkos: Add "#ifdef ALLOW_NON_DETERMINISTIC_SSA" toggle
...
SSA atom binning algorithm was adjusted to do as much work in
parallel while preserving deterministic behavior. The final
step is done serially to preserve deterministic behavior.
An alternative would be to sort the contents of the bins so
that they are always in the same order.
2017-02-28 12:53:56 -05:00
2b78ac2146
USER-DPD Kokkos: Add "#ifdef DPD_USE_RAN_MARS" toggle
...
Also, initialize the rand_pool with a seed in init_style()
2017-02-28 12:49:11 -05:00
9736fb3be8
added sucrose latte min example
2017-02-28 10:40:46 -07:00
a5507b291d
USER-DPD Kokkos: give each workItem index a unique instance of RanMars
...
Makes fix_shardlow_kokkos deterministic across runs and thread count.
2017-02-26 18:00:20 -05:00
3eba3e5a1b
USER-DPD Kokkos: for deterministic results, serialize bin_atoms() for now.
2017-02-26 17:57:13 -05:00
e4b544f934
Make pair_dpd_fdt_energy's random seed public so fix_shardlow can use it.
2017-02-26 17:53:45 -05:00
35ee24cfad
use RandWrap in pair_dpd_fdt_energy_kokkos and fix_shardlow_kokkos
2017-02-26 14:50:58 -05:00
e4500859a3
USER-DPD: add "#ifdef DEBUG_PAIR_CT" debugging code to fix_shardlow*
2017-02-24 22:24:29 -05:00
fd1523c756
USER-DPD Kokkos: add missing () in STACKPARAMS check in ssa_update_*
2017-02-24 22:19:53 -05:00
21619b2976
USER-DPD Kokkos: correct the setup of the ghost SSA workplan
2017-02-24 22:16:33 -05:00
b053c367ea
USER-DPD Kokkos: remove extranious debugging code
2017-02-24 19:09:07 -05:00
c2e3a76225
USER-DPD Kokkos: rand seed can't be zero, so add some salt.
2017-02-24 19:07:55 -05:00
6ea290a699
DEBUG: make FixShardlowKokkos have it's own rand_pool, plus debug code.
...
ssa_update_dpde() hangs on first use of rand_gen.normal()
Switching to not using a pointer to PairDPDfdtEnergyKokkos's rand_pool
had no noticble effect.
2017-02-24 17:41:57 -05:00
c56e0692b9
USER-DPD Kokkos: enable install of SSA Kokkos code
2017-02-24 17:38:46 -05:00
71379487ab
USER-DPD: variety of fixes for new SSA Kokkos code. Still not functional.
2017-02-24 17:35:58 -05:00
f7a48719ad
USER-DPD: first attempt at fix_shardlow_kokkos... It compiles!
2017-02-24 13:35:48 -05:00
a341a6bca9
USER-DPD: make locals & ghosts use similar SSA work plan data structure
...
Kokkos SSA won't use AIRct_ssa[], but still used for non-Kokkos for now.
2017-02-24 13:27:27 -05:00
2f04e87d07
USER-DPD: make PairDPDfdtEnergyKokkos's rand_pool public so it can be reused
2017-02-24 13:24:18 -05:00
aecafecaa2
USER-DPD: fix missing host prefixes in AtomVecDPDKokkos::pack_comm
2017-02-24 13:21:26 -05:00
1db62a57b5
USER-DPD: pair_dpd_fdt_energy_kokkos: enable STACKPARAMS specialization
2017-02-24 13:17:49 -05:00
2dcbc805ba
min latte partially fixed
2017-02-23 18:20:02 -07:00
b27cc8f474
USER-DPD: use LAMBDA instead of functor for ghost binning in nbin_ssa_kokkos
2017-02-22 15:08:24 -05:00
8065d96761
USER-DPD: first attempt at npair_ssa_kokkos... It compiles!
2017-02-22 15:08:24 -05:00
01d0a5c4a2
BUGFIX: use Kokkos::atomic_fetch_max() to avoid a race on new_maxneighs
2017-02-22 15:08:24 -05:00
5c6e7b12c6
BUGFIX: fix a copy-o in build_Item_Ghost(): xbin2, etc. should be an int
...
xbin2, ybin2, and zbin2 are temporary integer bin coordinates, not floats!
2017-02-22 15:08:24 -05:00
19ffe59315
USER-DPD: fix typo in NPairHalfBinNewtonSSA::build(): sz1 instead of sx1
...
Luckily, no real change, since sz1 and sx1 are normally identical.
2017-02-22 15:08:23 -05:00
37810bdc53
USER-DPD: move centroid bin of stencil_ssa to the first slot.
...
Eliminates a special case version of a loop just for Subphase 0.
NOTE: pair evaluation order changes, causing numerical differences!
This changed the order that close neighbors of ghosts are processed.
2017-02-22 15:08:23 -05:00
7feb6c2853
USER-DPD: fix a bug in AtomVecDPDKokkos::unpack_restart()
2017-02-22 15:08:23 -05:00
d1a0a3e1c3
USER-DPD: first attempt at nbin_ssa_kokkos... It compiles!
2017-02-22 15:08:22 -05:00
c2ee3285fc
USER-DPD: change nstencil_ssa[] to eliminate a corner case
...
Saves a conditional inside an NPairHalfBinNewtonSSA::build() inner loop
2017-02-22 15:08:22 -05:00
5289ec0b39
cleanup: remove unused binatomsItem() declaration in npair_kokkos.h
2017-02-22 15:08:22 -05:00
e0bafa499d
indentation fixes in npair_kokkos.cpp, plus a comment question
2017-02-22 15:08:22 -05:00
4b3197202b
USER-DPD: Rework SSA to use a new neighbor list structure, ready for Kokkos
...
NOTE: pair evaluation order changes, causing numerical differences!
Atom pair processing order is fully planned out in npair_half_bin_newton_ssa
Makes the SSA neighbor list structure very different. Do not use by others!
Each local is in ilist, numneigh, and firstneigh four times instead of once.
Changes LAMMPS core code that had been previously changed for USER-DPD/SSA:
Removes ssaAIR[] from class Atom as it is now unused.
Removes ndxAIR_ssa[] from class NeighList as it is now unused.
Increases length of ilist[], numneigh[], and firstneigh[] if SSA flag set.
2017-02-22 15:08:21 -05:00
ab32d136b9
USER-DPD: SSA with Kokkos: make stencil's sx, sy, sz variables public
2017-02-22 15:08:21 -05:00
151b3f552b
USER-DPD: Save pointer to the NPair used to create the NeighList
...
Gives a user of NeighList access to data stored in a custom NPair
2017-02-22 15:08:21 -05:00
52aaad907f
USER-DPD: SSA with Kokkos: Reorder stencil subphases to make things easier.
2017-02-22 15:08:20 -05:00
be166cb5bf
USER-DPD: Use subphases when processing AIR zero (locals) in SSA.
...
NOTE: pair ordering was NOT changed, but tiny differences could occur.
2017-02-22 15:08:20 -05:00
ee83b755ea
USER-DPD: Split the SSA stencil and neighbor list into subphases.
...
NOTE: pair evaluation order changes, causing numerical differences!
This enables processing neighbors in subphase groups that enforce
a geometrical seperation of pairs, allowing greater parallelism
once fix_shardlow (SSA) is converted to Kokkos.
2017-02-22 15:08:20 -05:00
ce2da5068b
USER-DPD: renumber AIRs back to 1-7 for ghosts, and just 0 for locals.
...
This removes the the distinction between pure and impure locals.
Pure and impure locals messed up the directionality of half neighbor lists,
which turns out is crucial to the approach for SSA with kokkos.
2017-02-22 15:08:19 -05:00
641bb4bb16
USER-DPD: remove use of ssaAIR[], move coord2ssaAIR() to nbin_ssa.cpp
...
Saves an int per atom and ghost, also simplifies and reduces code size.
2017-02-22 15:08:19 -05:00
f73c9a43ab
USER-DPD: remove broken code for building SSA half neighbor list from full
2017-02-22 15:08:19 -05:00
3dddeef365
USER-DPD: remove unneeded gairct_ssa[] & anum vars, and some > 0 guards
2017-02-22 15:08:19 -05:00
fb279a87f5
USER-DPD: properly compute AIRct_ssa values, and use them in fix_shardlow.
...
Eliminates last use of per-atom ssaAIR values within initial_integrate()
2017-02-22 15:08:18 -05:00
e9d46f4e7a
USER-DPD: Correct an error message typo.
2017-02-22 15:08:18 -05:00
e42678ed51
USER-DPD: track & use the extent of the local atoms in the bins
2017-02-22 15:08:18 -05:00
ff2786c86c
USER-DPD: Make another version of coord2bin() for nbin_ssa
2017-02-22 15:08:17 -05:00
6384486764
USER-DPD: Copy inline coord2bin() functions from nbin_kokkos into nbin_ssa
2017-02-22 15:08:17 -05:00
0512e78860
USER-DPD: new neighbor list code for SSA that gives neighbors to ghosts.
...
This simplifies the processing of the neighbor list in fix_shardlow.
NOTE: pair evaluation order changes, causing numerical differences!
2017-02-22 15:08:17 -05:00
2db66e49b4
USER-DPD: make pair_dpd_fdt* check more generically for use of fix_shardlow
...
Allows easier experimentation of alternative shardlow implementations.
2017-02-22 15:08:17 -05:00
e76cad358b
Merge branch 'FixRX_Kokkos_merge' into USER-DPD_kokkos
2017-02-22 14:25:41 -05:00
0a751c5901
KOKKOS: fix a compile-time error caused by merge of patch 21Feb17
...
Remove the unused PairHybridOverlayKokkos::modify_requests() method
The patch removed the parent PairHybridOverlay::modify_requests()
2017-02-22 11:52:20 -05:00
83988a1026
Merge branch 'master' into USER-DPD_kokkos as of patch 21Feb17
2017-02-22 11:29:01 -05:00
acc5bde0fe
Removed printf's from FixRXKokkos and FixRX.
...
- Commented out the printf's in FixRXKokkos and FixRX used for
active debugging.
2017-02-13 16:36:30 -05:00
799d55e097
Switched to operator()'s and Tag's for the Kokkos launch objects.
...
- Switched from using lambda functions to operator()'s with type tags
in FixRxKokkos. The lambda's were giving big problems in Cuda with
the memory objects. This required that all referenced views be members
of the FixRXKokkos class.
- Add copymode controls to solve_reactions() to avoid the destructor
freeing pointers carried forward from the copy constructor. Added
the same to FixRX since its called, too.
2017-02-13 16:33:21 -05:00
4e9c8f4962
Update FixRXKokkos for Cuda build. Added inline and other KOKKOS macros.
...
- Updated the function prototypes to include the necessary KOKKOS
macros for __host__ and __device__ functions and inlined functions.
- Changed several View definitions to match the disjoint memory spaces
that only come up with Cuda builds.
2017-02-13 16:33:21 -05:00
2f32c1a9af
Switched to using Kokkos device data for ODE scratch data.
...
- Finished porting all scratch arrays to using the StridedArrayType
template.
- Created a single, large Kokkos device array and using that for all
scratch data passed into the StridedArrayType objects.
2017-02-13 16:33:20 -05:00
4ac7a5d1f2
Added Kokkos-like array datatype into RK4 and RHS in FixRXKokkos.
...
- Created an Array class that provides stride access for operator[]
w/o needing Kokkos views. This was designed to avoid the performance
issues encountered with Views and sub-views throughout the RHS and
ODE solver functions.
2017-02-13 16:33:20 -05:00
93d99ec8d0
Added ODE diagnostics to FixRxKokkos using Kokkos managed data.
...
- Added the diagnostics performance analysis routine to FixRxKokkos
using Kokkos views.
TODO:
- Switch to using Kokkos data for the per-iteration scratch data.
How to allocate only enouch for each work-unit and not all
iterations? Can the shared-memory scratch memory work for this,
even for large sizes?
2017-02-13 16:33:19 -05:00
4e8351d9c8
Code clean-up for FixRxKokkos.
...
- Removed dead code and old errors.
TODO:
- Per-thread scratch data in kokkos.
- ODE Diagnostics in kokkos.
2017-02-13 16:33:19 -05:00
f2d005fb8d
Fixed errors in FixRxKokkos kokkos neighbor lists initialization and
...
usage and calls to computeLocalTemperature.
- Created request for kokkos neighbor list for fix and switched to
that neighbor list datatype in computeLocalTemperature.
- Reconfigured pre_force and setup_pre_force to call a common
solve_reactions() method to avoid duplicate code.
TODO:
- Clean-up
- Provide per-problem scratch data within kokkos framework (instead
of C++ new/delete data).
2017-02-13 16:33:18 -05:00
0d57a1d831
Added setup_pre_force, pack/unpack methods to FixRxKokkos.
...
- Added a kokkos version of setup_pre_force that only sets dvector
and then communicates that.
- Converted all for loops to parallel_for's in computeLocalTemperator()
and setup_pre_force.
- Added pack/unpack forward/reverse methods with Kokkos host views.
TODO:
- The Kokkos neighbor list is not working. Need to request a Kokkos
neighbor list in ::init(). Then, replace objects like list->ilist[]
with k_list->d_ilist().
2017-02-13 16:33:18 -05:00
acba25c383
Added kokkos datatypes to FixRxKokkos::computeLocalTemperature(...)
...
Added kokkos dual-view datatypes used in computeLocalTemperature and
pre_force (e.g., dpdThetaLocal) but still using the original host
pointers for the pack/unpack operations.
TODO:
- The Kokkos neighbor list is not working. Need to request a Kokkos
neighbor list in ::init(). Then, replace objects like list->ilist[]
with k_list->d_ilist().
- Add another template parameter for HALFTHREAD and create (automatic)
atomic view of dpdThetaLocal and sumWeights.
- Add modify/sync comments and replace the host-only pointers in the
pack/unpack methods.
2017-02-13 16:33:17 -05:00
843f3a9192
Updates to FixRxKokkos ...
...
- Added templated computeLocalTemp<>() to FixRxKokkos but still
using the original host data pointers.
- Updated the copy-back to dvector operation to be the same with
RK4 and RKF45 per discussion with J. Larentzos.
TODO:
- Add kokkos data for computeLocalTemp and parallel_for loop.
2017-02-13 16:33:15 -05:00
2ea900df00
Updated FixRxKokkos to use kokkos-managed data objects.
...
- Switched to use kokkos dvector, mask, and dpdTheta views
from atomKK.
2017-02-13 16:33:13 -05:00
70fa9189a8
Updated KOKKOS installer and updated USER-DPD FixRx to match KOKKOS version.
...
- Updated the KOKKOS installer to include the fix_rx_kokkos.[cpp,h].
- Updated the USER-DPD version of fix_rx.[cpp,h] to sync with the Kokkos
version. Solves child->parent class dependencies.
2017-02-13 16:33:09 -05:00
41d3903f5a
Added kokkos-managed parameters for FixRxKokkos.
...
- Added kokkos-managed parameter data for the kinetics equations.
- Removed dependencies in rhs() on atom and domain objects.
TODO:
1. Switch to using KOKKOS data for dvector.
2. Port ComputeLocalTemp(...) to Kokkos (needs pairing algorithm).
2017-02-13 16:33:05 -05:00
43d61f313f
Initial bare-bones port of FixRX to Kokkos.
...
Initial port of USER-DPD/fix_rx.cpp to KOKKOS/fix_rx_kokkos.cpp.
Using parallel_reduce(...) but still using host-only data.
TODO:
1. Switch to KOKKOS datatypes for sparse-kinetics data; dense
is finished.
2. Switch to using KOKKOS data for dvector.
3. Remove dependencies in rhs(...) on atom. Store those consts
in UserData{} or as member constants.
4. Port ComputeLocalTemp(...) to Kokkos (needs pairing algorithm).
2017-02-13 16:33:02 -05:00
dc16228a60
Merge branch 'USER-DPD_ssa_update' into USER-DPD_kokkos
2017-02-13 15:03:14 -05:00
96a43e8ef1
Merge branch 'master' into USER-DPD_kokkos as of patch 13Feb17
2017-02-13 12:29:41 -05:00
dc9c2399b2
Merge branch 'master' into USER-DPD_kokkos
...
Fixed trivial merge conflict in src/KOKKOS/Install.sh
2017-02-06 15:45:26 -05:00
b3e9006aef
Merge branch 'master' into USER-DPD_kokkos
2017-01-30 12:04:30 -05:00
a1f4551ac2
Adding missing sync/modified in atom_vec_dpd_kokkos
2017-01-27 10:18:41 -07:00
f3c5919606
Merge remote branch 'upstream/master' into USER-DPD_kokkos
2017-01-27 08:08:05 -07:00
ebe27c65e1
Removing duplicate code in pair_exp6_rx_kokkos
2017-01-26 10:33:03 -07:00
85c8db5f86
Fixing warning in pair_dpd_fdt_energy_kokkos
2017-01-26 10:10:52 -07:00
be13ecfa17
Fixing Kokkos warnings
2017-01-26 10:10:42 -07:00
6cc969db92
Fixing warnings in Kokkos
2017-01-26 09:24:13 -07:00
8050eb3aa8
Another tweak to sync/modify in pair_multi_lucy_rx_kokkos
2017-01-26 09:17:59 -07:00
c617bc180a
Adding sync/modify to pair_multi_lucy_rx_kokkos
2017-01-26 08:52:17 -07:00
8e808f6c6b
Zeroing variables in pair_exp6_rx_kokkos to match pull request
2017-01-24 11:45:27 -07:00
5897955e2e
Fixing GPU memory issue in fix_eos_table_rx_kokkos
2017-01-24 11:24:47 -07:00
f9bc81b924
Merge branch 'master' into USER-DPD_kokkos as of patch 20 Jan 2017.
2017-01-20 16:43:13 -05:00
0887ff1273
Merge pull request #13 from timattox/master
...
simplified neighbor list copying, merge from Master branch, merged #13 .
2017-01-20 09:37:07 -07:00
521f3df3d5
Initialize variables in pair_exp6_rx_kokkos
2017-01-19 16:54:50 -07:00
6d47cf350c
Makefile for latte_dev
2017-01-19 15:42:09 -07:00
de6442d845
Fixing GPU memory issues in Kokkos
2017-01-19 11:55:22 -07:00
917ca19b34
Fixing GPU memory issue in modify_kokkos, need to cherry pick back to Master
2017-01-19 09:54:15 -07:00
cf83ce4543
Adding zero compute to pair_dpd_fdt_energy_kokkos
2017-01-19 08:44:30 -07:00
116ae9d0c4
Fixing copy bug in pair_exp6_rx_kokkos
2017-01-18 14:51:35 -07:00
e05b132289
Fixing error check in fix_eos_table_rx_kokkos
2017-01-18 14:18:35 -07:00
4f2fcee6df
Merge branch 'master' into USER-DPD_kokkos as of 3af4b3c28 on 18 Jan. 2017
...
Includes a critical bugfix for using USER-DPD and MOLECULE together.
2017-01-18 15:08:32 -05:00
2d32fa8ccb
Fixing GPU memory issues in atom_vec_dpd_kokkos
2017-01-18 12:53:40 -07:00
b38733e5a2
Fixing GPU memory issue in pair_exp6_rx_kokkos
2017-01-18 10:15:06 -07:00
96636c7514
Fixing warnings in pair_exp6_rx_kokkos
2017-01-17 16:43:55 -07:00
5569c4c130
Fixing GPU memory issue with fix_property_atom_kokkos
2017-01-17 16:19:25 -07:00
8b4130c0cb
Fixing issue with pressure in pair_hybrid_kokkos
2017-01-17 13:28:55 -07:00
91d68e26ef
Prevent overlapping host/device computation in pair_hybrid_kokkos
2017-01-17 12:26:00 -07:00
883385c8e4
Merge branch 'master' into USER-DPD_kokkos as of patch 17Jan17
2017-01-17 13:19:06 -05:00
e3153e0b30
Merge pull request #12 from ibaned/pair-table-rx-kokkos
...
fix CUDA type issues in pair_table_rx_kokkos
2017-01-13 14:43:48 -07:00
688df1c254
fix CUDA type issues in pair_table_rx_kokkos
...
stop using the global DAT, use the pair's
DeviceType for all the relevant types.
2017-01-13 14:40:36 -07:00
2b2998052c
Fixing inheritance issue in pair_hybrid_overlay_kokkos
2017-01-13 13:50:21 -07:00
dc1b94cdd2
Merge pull request #11 from ibaned/pair-table-rx-kokkos
...
support for eatom and vatom in pair_table_rx_kokkos
2017-01-13 13:27:48 -07:00
a42a666142
support for eatom and vatom in pair_table_rx_kokkos
2017-01-13 13:23:26 -07:00
f16f9393ef
Merge branch 'master' into USER-DPD_kokkos
2017-01-13 10:51:28 -07:00
2a35fa7a4e
Adding initial versions of pair_hybrid_kokkos and pair_hybrid_overlay_kokkos
2017-01-13 10:37:31 -07:00
c15d6580da
Fixing issue in pair_multi_lucy_rx_kokkos found by ibaned
2017-01-13 10:01:22 -07:00
1ae53d59fa
Merge pull request #9 from ibaned/pair-table-rx-kokkos
...
pair_table_rx_kokkos from @ibaned
2017-01-13 09:26:30 -07:00
aaa7dca21b
Makefile.lammps.gfortran
2017-01-12 17:13:02 -07:00
6bd17be454
Makefile.lammps.gfortran
2017-01-12 16:58:27 -07:00
5b7ab135dd
Fixing Kokkos neighbor bug
2017-01-12 16:36:27 -07:00
0635151e2d
Fixing neighbor bug
2017-01-12 16:36:04 -07:00
cce10f6dff
remove more leftover code
2017-01-12 14:19:10 -07:00
4dab6737ba
remove leftover code
2017-01-12 14:15:42 -07:00
0c3b942686
cleanup changes to Install.sh
2017-01-12 13:50:30 -07:00
f51ddf8450
Makefile.lammps.gfortran
2017-01-12 13:50:02 -07:00
3580e5409d
Fixing Kokkos CUDA compile error
2017-01-12 09:00:07 -07:00
b7d0dc8440
Merge branch 'debug' into pair-table-rx-kokkos
2017-01-12 08:32:51 -07:00
52761aee0d
it compiles.
2017-01-11 13:18:13 -07:00
5dcbbba4ce
lots of work towards compiling
2017-01-11 13:15:01 -07:00
fdb6b91e29
near trying to compile
2017-01-11 12:50:32 -07:00
41804ff524
progress converting compute_style
2017-01-11 12:42:05 -07:00
c2bb20e60f
made compute_fpair a free function as well
2017-01-11 11:54:01 -07:00
cb9fdf7801
starting to separate compute_item from the class
2017-01-11 11:44:54 -07:00
b5ff41f5ef
made MixingWeights code non-member
...
CUDA was simply giving too many
errors dealing with captures of
member variables.
2017-01-11 11:10:33 -07:00
6a9a0e8c33
tracking down some invalid reads...
2017-01-11 09:25:13 -07:00
d65676e981
make everything public to appease NVCC
2017-01-10 16:08:55 -07:00
55aa91be6b
copy uCG and uCGnew correctly
2017-01-10 15:28:19 -07:00
5d5751be19
fix class name in PAIR_CLASS setup
2017-01-10 15:28:19 -07:00
e4673d7fa8
fix compilation
2017-01-10 15:28:19 -07:00
c877c07491
progress towards custom compute functor
...
which is needed to handle uCG contributions.
2017-01-10 15:28:19 -07:00
4d5abe64d5
draft compute_fpair for PairTableRXKokkos
2017-01-10 15:28:19 -07:00
afbc6fc628
added coeff, settings, single, fix compile
2017-01-10 15:28:19 -07:00
21cde6261a
add member variables from PairTableRX
2017-01-10 15:28:19 -07:00
f995bb4335
starting to add getMixingWeights
...
some compile errors to work out
2017-01-10 15:28:19 -07:00
6abefe7ef9
restarting PairTableRXKokkos
...
as an exact copy of PairTableKokkos,
now that it derives from PairTable
2017-01-10 15:28:19 -07:00
98c66089a9
Merge pull request #8 from ibaned/pair-multi-lucy-rx-kokkos-rho
...
fix race condition on rho, thanks @ibaned
2017-01-10 15:25:21 -07:00
d26f1403cd
fix race condition on rho
...
the main bug here is the use of a local
rho_i accumulator which later gets assigned
back to rho[i].
in parallel, atomic additions can happen to
rho[i] while the local accumulator is held;
those atomic additions are lost when
the accumulator is atomically assigned.
we instead initialize the accumulator to zero
and atomically add it back to rho[i].
2017-01-10 15:22:52 -07:00
1f6cfb1b31
Makefile.lammps.gfortran changed
2017-01-10 10:56:31 -07:00
001964ecd8
Merge branch 'ibaned-pair-table-rx-inherit' into USER-DPD_kokkos
2017-01-09 14:04:31 -05:00
9807062594
Merge branch 'pair-table-rx-inherit' of https://github.com/ibaned/lammps into ibaned-pair-table-rx-inherit
2017-01-09 13:39:44 -05:00
26d50853e9
Merge branch 'master' as of patch 6Jan17 into USER-DPD_kokkos
2017-01-09 13:12:02 -05:00
7201f003e5
move another enum back
...
see lammps/lammps#325
2017-01-05 21:00:39 -07:00
d8ddef37ed
put enum back in .cpp file
...
see lammps/lammps#325
2017-01-05 20:56:37 -07:00
ad1402562d
Revert "move enum to pair.h"
...
This reverts commit a1ac2ae9b7
2017-01-05 20:54:24 -07:00
70927d08e7
remove duplicate enum
2017-01-05 20:53:45 -07:00
a1ac2ae9b7
move enum to pair.h
...
to avoid having it be replicated
in several different locations
2017-01-05 20:53:45 -07:00
3941fe9ab7
fix compilation
2017-01-05 20:53:45 -07:00
318ab9a185
trying PairTableRX : public PairTable
...
saves a lot of duplicate code
2017-01-05 20:53:45 -07:00
49d644ec3a
Merge pull request #7 from ibaned/pair-dpd-energy-kokkos-warnings
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fix many warnings in pair_dpd_fdt_energy_kokkos
2017-01-05 16:46:04 -07:00
e5906dfba0
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
2017-01-05 15:37:21 -07:00
967cdd947e
cleanup
2017-01-05 15:37:01 -07:00
19f2d2d1ec
fix many warnings in pair_dpd_fdt_energy_kokkos
...
one Kokkos kernel was not annotated consistently,
STACKPARAMS was essentially uninitialized and
confused with a local variable,
plus lots of variables were unused in some
of the Kokkos kernels.
2017-01-05 15:34:05 -07:00
332372dec2
Renamed Makefile.afrl_thunder to Makefile.icex to be more general.
2017-01-05 14:03:16 -05:00
8503ac22a8
Fixed error->all instead of error->one bug in USER-DPD/fix_shardlow.cpp.
...
During dynamic load balancing, the subdomains will not be uniform so the
bbox size test in USER-DPD/fix_shardlow.cpp may only be called by one rank.
Using error->one allows any rank to stop the simulation in this scenario.
Added rcut and bbox information to help in diagnostics.
2017-01-05 13:58:11 -05:00
cc4040de10
Merge remote-tracking branch 'origin/USER-DPD_kokkos' into USER-DPD_kokkos
2017-01-05 12:25:45 -05:00
a4271ae8c5
Added a Makefile for AFRL Thunder.
2017-01-04 15:13:46 -05:00
79ed1b5258
Merge branch 'USER-DPD_updates' into USER-DPD_kokkos, bring over history.
2017-01-03 17:04:12 -05:00
b5c7d44299
Merge branch 'USER-DPD_kokkos_updates' into USER-DPD_kokkos
2017-01-03 12:35:24 -07:00
fe3c98cdbb
Merge pull request #4 from ibaned/dpd-fixes
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some warning fixes
2017-01-03 14:29:11 -05:00
50df3da343
Merge pull request #3 from ibaned/fix-dpd-energy-kokkos-pr
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Implement a Kokkos version of fix_dpd_energy
2017-01-03 14:27:49 -05:00
ae0e882cde
Updating pair_multi_lucy_rx_kokkos to USER-DPD changes
2017-01-03 11:51:28 -07:00
6d7607a6ad
member function containing lambdas must be public
2017-01-03 11:50:44 -07:00
e3ebd8e7f1
remove syncs that shouldn't be needed
2017-01-03 11:50:44 -07:00
dae132c770
place newline at end of file
2017-01-03 11:42:40 -07:00
e632f8597a
fix warning about enum comparisons
2017-01-03 11:42:39 -07:00
89795b3653
got fix_dpd_energy_kokkos to compile
2017-01-03 11:41:40 -07:00
04e2f170a3
first draft fix_dpd_energy_kokkos
...
had to make k_duCond and k_duMech
in pair_dpd_fdt_energy_kokkos
public so they could be accessed
and sync'ed
2017-01-03 11:41:40 -07:00
53e07996c6
save draft of fix_dpd_energy_kokkos.cpp
2017-01-03 11:41:39 -07:00
66cdd3a708
draft fix_dpd_energy_kokkos.h
2017-01-03 11:41:39 -07:00
ccaa0506cb
LAMMPS_LAMBDA from ibaned/lammps@7559bc9
2017-01-03 11:41:39 -07:00
f220b07625
Updating pair_exp6_rx_kokkos to USER-DPD changes
2017-01-03 10:36:55 -07:00
2af10cb8da
Updating fix_eos_table_rx_kokkos to USER-DPD changes
2017-01-03 10:09:44 -07:00
cc1b55e031
Merging USER-DPD updates
2016-12-23 12:36:05 -07:00
a36e563aa5
Temporarily reverting change to pair_table_kokkos to allow runtime testing
2016-12-22 14:37:42 -07:00
a4ab877c46
Change to allow pair_dpd_fdt_energy_kokkos
2016-12-22 13:16:57 -07:00
f6fe61196d
CPU runtime tested version of pair_multi_lucy_rx_kokkos
2016-12-22 11:34:17 -07:00
163b61a32e
Removing pair_table_rx_kokkos from Kokkos Install.sh since it isn't ready for runtime testing
2016-12-21 15:37:00 -07:00
26c21da45b
Merge branch 'master' into USER-DPD_kokkos as of 21Dec16 patch
2016-12-21 16:50:42 -05:00
807d9529da
Fixing issues found during GPU runtime testing
2016-12-21 10:41:29 -07:00
73326922d6
Fixing Kokkos issue in fix_eos_table_rx_kokkos
2016-12-21 08:56:48 -07:00
35803c75c9
Fixing issues found during GPU runtime testing
2016-12-20 17:03:46 -07:00
07bee39002
Merge branch 'USER-DPD_whitespace' into USER-DPD_kokkos
2016-12-20 12:23:02 -05:00
889ee78f8b
Change necessary for pair_exp6_rx_kokkos to compile on GPU
2016-12-19 17:15:02 -07:00
f62a6fe5a5
Renaming rand_pool_wrap to rand_pool_wrap_kokkos
2016-12-19 16:50:22 -07:00
6f51c3b75c
Fixing issues in pair_multi_lucy_rx_kokkos
2016-12-19 16:25:31 -07:00
99910fc432
Adding CPU runtime tested version of pair_dpd_fdt_energy_kokkos
2016-12-19 15:27:16 -07:00
000df6e1cf
Fixing what seems to be a Kokkos bug, I will submit to Kokkos lib developers too
2016-12-19 15:20:10 -07:00
3f1f51c1c7
Changes necessary for runtime testing of Kokkos styles
2016-12-19 13:31:09 -07:00
21bb603b93
Porting recent changes from USER-DPD package to KOKKOS package
2016-12-19 13:30:00 -07:00
ac57f4721c
Small whitespace tweak to pair_dpd_fdt_energy
2016-12-16 17:14:27 -07:00
5cae3eca8c
Whitespace cleanup to pair_dpd_fdt_energy, should be cherry-picked to Master
2016-12-16 17:09:19 -07:00
8474453efd
Merge branch 'master' into USER-DPD_kokkos: as of 17Dec16 patch
2016-12-16 15:02:41 -05:00
cfa61b98ae
Fixing runtime issues in fix_eos_table_rx_kokkos
2016-12-16 12:37:41 -07:00
d93e3d1cee
Fixing runtime issues with pair_exp6_rx_kokkos
2016-12-16 10:06:12 -07:00
f47a40b2e4
Fixing Kokkos memory deallocation issue
2016-12-16 10:02:01 -07:00
a3c1d385e8
Adding Kokkos version of fix_property_atom
2016-12-15 15:50:30 -07:00
d5f8f36442
Change to fix_property_atom to allow virtual override of grow_arrays() function
2016-12-15 15:48:09 -07:00
c0d6cbbdd3
Updates to Kokkos files
2016-12-15 11:18:50 -07:00
a58f7631c0
fix_latte unpdated
2016-12-15 10:57:02 -07:00
a9d26b3f4a
Updates to Kokkos files
2016-12-14 12:58:02 -07:00
cf4010474d
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
2016-12-14 12:50:52 -07:00
766b3fa457
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
...
Sync all changes made in lammps master branch with exaalt branch
2016-12-14 11:49:49 -07:00
ee4d1b340b
test push
2016-12-14 11:48:06 -07:00
07d9f9d66e
updated version of fix latte from SJP
2016-12-14 11:48:06 -07:00
f209c8c129
changes in fix_latte
2016-12-14 11:48:06 -07:00
ef8d507338
changes in latte makefile for lattelib and README
2016-12-14 11:48:06 -07:00
e59552c2ec
changes for lattelib
2016-12-14 11:48:06 -07:00
7eb05b33fb
initial dummy version of fix_latte.cpp
2016-12-14 11:48:06 -07:00
3e2cd6d265
Merging from master to 13Dec16 version
2016-12-14 11:46:04 -07:00
544e23f971
test push
2016-12-14 11:38:39 -07:00
16b15a636c
updated version of fix latte from SJP
2016-12-14 11:38:39 -07:00
d43bd57a40
changes in fix_latte
2016-12-14 11:38:39 -07:00
b912db5c73
changes in latte makefile for lattelib and README
2016-12-14 11:38:39 -07:00
765fe3cdfe
changes for lattelib
2016-12-14 11:38:39 -07:00
031d4acde8
initial dummy version of fix_latte.cpp
2016-12-14 11:38:39 -07:00
d47c6b2761
Merge branch 'master' into USER-DPD_kokkos
2016-12-14 11:25:11 -07:00
f93c62d3e2
Reverting accidental change
2016-12-13 16:54:00 -07:00
1dbf6d443f
Adding Kokkos files
2016-12-13 16:43:40 -07:00
5f78c2b6a5
test push
2016-12-01 15:14:47 -07:00
45b85b1686
updated version of fix latte from SJP
2016-12-01 14:50:11 -07:00
3f68d370b5
Merge branch 'master' into USER-DPD_kokkos: up to date to 30Nov16 patch
2016-11-30 16:57:48 -05:00
6e6776f396
Finish moving/integrating atom_vec_dpd_kokkos into the Kokkos package
2016-11-30 16:25:07 -05:00
fe99fc287d
changes in fix_latte
2016-11-28 15:29:37 -07:00
6d94439cfe
Integrating pair_dpd_fdt_energy_kokkos files
2016-11-28 14:42:47 -07:00
91e38720d5
Adding pair_exp6_rx_kokkos files
2016-11-28 14:25:02 -07:00
7590791604
Integrating atom_vec_dpd into the Kokkos package
2016-11-21 13:54:14 -07:00
8f78157202
USER-DPD: aplly unpack_comm_hybrid bugfix d31121b to atom_vec_dpd_kokkos.cpp
2016-11-21 12:32:48 -05:00
1d939231a4
USER-DPD: initial Kokkos port, first steps from Aug 24th ARL Kokkos hackathon
...
atom_vec_dpd_kokkos
pair_dpd_fdt_energy_kokkos without the Oct 7th VV support from e27ed6c
2016-11-21 12:21:01 -05:00
f040f15218
changes in latte makefile for lattelib and README
2016-11-14 16:11:12 -07:00
f3d6ecf07b
changes for lattelib
2016-11-14 07:58:47 -07:00
6f23f6535c
initial dummy version of fix_latte.cpp
2016-11-09 13:48:11 -07:00
