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17516 Commits

Author SHA1 Message Date
Rupert Nash 1bb18ebde4 rollback unneeded change to Makefile.list per review 2019-06-21 15:50:52 +01:00
Rupert Nash 26347ec80c Add docs for compute momentum 2019-06-19 13:56:00 +01:00
Rupert Nash 959da9de01 Create a compute for the momentum of a group of atoms 2019-06-19 13:56:00 +01:00
Axel Kohlmeyer bb11344424
Merge pull request #1522 from akohlmey/next_version 
Step version string for next patch release
 2019-06-18 22:01:42 -04:00
Axel Kohlmeyer e754fb80a4
Merge pull request #1518 from akohlmey/collected-small-changes 
Collected small changes and fixes for the next patch release
 2019-06-18 16:21:41 -04:00
Axel Kohlmeyer 98fbaef406
workaround for ICE issue with gcc 4.8.x 2019-06-18 15:00:27 -04:00
Axel Kohlmeyer d98c105d34
step version string to 18 June 2019 2019-06-18 11:52:09 -04:00
Axel Kohlmeyer 961dcfc261
mention alternate build environment generators for cmake 2019-06-18 11:50:06 -04:00
Axel Kohlmeyer 81cdce9b04
flag and document that USER-TALLY computes are not compatible with dynamic groups 2019-06-18 00:14:48 -04:00
Axel Kohlmeyer 995b6b31a2
flag a couple more packages that contain sub-builds of downloaded code 2019-06-17 16:05:54 -04:00
Axel Kohlmeyer e9666f585f
update log files for kolmogorov/crespi/full potential 2019-06-17 15:46:54 -04:00
Axel Kohlmeyer f4f4a7c850
adapt for Ninja build tool, which cannot handle sub-builds and fortran 
so builds of downloaded libraries are not supported right now
 2019-06-17 14:24:51 -04:00
Axel Kohlmeyer 5fc3081a55
make building tools (msi2lmp, chain.x) an option, which is off by default 2019-06-17 14:23:30 -04:00
Axel Kohlmeyer a39a35af20
Merge pull request #1517 from jrgissing/bond/react-clarify-template-check-messages 
Bond/react: clarify reaction-template warning messages
 2019-06-17 14:14:53 -04:00
Axel Kohlmeyer 1452d3d25b
Merge pull request #1516 from gtribello/master 
Using PLUMED to compute committor with LAMMPS
 2019-06-17 14:14:37 -04:00
Axel Kohlmeyer 2dea4eb0e9
Merge pull request #1513 from akohlmey/user-tally-vs-hybrid 
Make USER-TALLY compute styles compatible with hybrid pair styles
 2019-06-17 14:14:06 -04:00
Axel Kohlmeyer 5d73b0790f
Merge pull request #1510 from evoyiatzis/respa_class_2 
Implementation of inner/middle/outer compute methods for lj/class2
 2019-06-17 14:13:47 -04:00
Axel Kohlmeyer 93fd33aad9
Merge pull request #1507 from athomps/yarray 
Back-porting of Zombie SNAP improvements
 2019-06-17 14:13:28 -04:00
Axel Kohlmeyer 6536399fc3
Merge pull request #1476 from uihsnv/log_spacing 
A function logfreq3(), for logarithmic spacing
 2019-06-17 14:12:59 -04:00
Axel Kohlmeyer 2f29bd29f4
Merge pull request #1430 from ndtrung81/gpu-neigh-hybrid 
Enable neighbor build on the device for pair hybrid substyles
 2019-06-17 14:12:40 -04:00
Axel Kohlmeyer b1458ceebf
fix typo 2019-06-17 07:42:18 -04:00
Axel Kohlmeyer 92615bda3a
update kolmogorov/crespi/full example input for recent change in REBO 2019-06-17 07:38:11 -04:00
Axel Kohlmeyer 4c0cd0a019
remove memory leak by freeing custom MPI data types 2019-06-17 07:36:03 -04:00
Axel Kohlmeyer fd93c27dcb
make valgrind happy by fully initializing line buffer for thermo output 2019-06-17 07:35:30 -04:00
jrgissing 4178c5167b clarify template error/warning message 2019-06-16 14:47:07 -06:00
Jacob Gissinger fd20a0606a
Merge pull request #49 from lammps/master 
rebase
 2019-06-16 14:19:50 -06:00
Gareth Tribello 75e2981bda Using force_timeout call instead of throwing error for plumed stop 2019-06-16 17:52:20 +01:00
Gareth Tribello 98d9a9a4d2 Added call to PLUMED with setStopFlag so that PLUMED can stop LAMMPS if it needs to. This would be needed if you were computing committors for example 2019-06-16 16:09:32 +01:00
Axel Kohlmeyer e73b34a5b1
do not run tally callback setup multiple times per time step 2019-06-14 15:46:28 -04:00
Axel Kohlmeyer ac57b41b4d
fix line endings and missing EOL at end 2019-06-14 07:13:06 -04:00
Evangelos Voyiatzis 43e3c1520b
cleaning pair_lj_class2.h of windows line endings 
removing DOS/Windows style CR/LF line endings
 2019-06-14 11:50:56 +02:00
Evangelos Voyiatzis e7116c8680
Update pair_class2.txt 
Addition of a few lines in the documentation file
 2019-06-14 09:04:03 +02:00
Aidan Thompson 4d7d3a5d53 Switched algorithm for compute_yi to one based on zlist ordering 2019-06-13 15:56:18 -06:00
Evangelos Voyiatzis c1550ba29b
implementation of inner/middle/outer for lj/class2 
Implementation of inner/middle/outer functions in style lj/class2 to enable integration with respa
 2019-06-13 22:23:01 +02:00
Aidan Thompson 5fb505ca8c Fixed typo 2019-06-13 10:24:18 -06:00
Aidan Thompson 67a1a63f5f Removed old text 2019-06-13 10:10:37 -06:00
Aidan P. Thompson 65b87fa278 Updated SNAP in KOKKOS package so it compiles and runs 2019-06-13 09:54:56 -06:00
athomps c5c03230cb
Not part of this pull request 2019-06-12 17:05:47 -06:00
athomps be5d3d6a19
Not part of this pull request 2019-06-12 17:04:22 -06:00
athomps f8e257d219
Not part of this pull request 2019-06-12 17:04:05 -06:00
athomps 3f523ea906
Not part of this pull request 2019-06-12 17:02:59 -06:00
Aidan Thompson a973700295 Completed back-porting of Zombie SNAP improvements, particularly noteworthy is reduction in memory footprint, elimination of most multidimensional arrays, elimination of diagonal_style, elimination of Z array in force calculation. 2019-06-12 16:42:28 -06:00
Axel Kohlmeyer daa53e3008
Merge pull request #1469 from julient31/pppm_spin 
Adding PPPM and Ewald solvers for electric dipoles and magnetic spins
 2019-06-12 14:50:18 -04:00
Stan Moore 7a33d1e328 Code cleanup 2019-06-12 11:36:42 -06:00
Aidan Thompson 0559e155f2 Implemented lists instead of multidim arrays 2019-06-11 18:24:02 -06:00
Axel Kohlmeyer 0b25d2feef
Merge pull request #1504 from akohlmey/collected-small-fixes 
Collected small bugfixes and changes
 2019-06-11 20:20:19 -04:00
Axel Kohlmeyer 1c1491eebf
Merge pull request #1506 from sniblett402/patch-1 
Bugfix for bond_style table with MPI
 2019-06-11 19:10:41 -04:00
Axel Kohlmeyer 400751f30f
remove redundant call to broadcast r0 2019-06-11 19:09:23 -04:00
sniblett402 4fbf96a353
Bugfix for bond_style table with MPI 
Summary

Very small bug fix - an incorrect MPI datatype was causing undefined behaviour for tabulated bond potentials (bond_style table).

Author(s)

Sam Niblett, LBNL

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

No impact

Implementation Notes

The equilibrium bond length of the tabulated potential (tb->r0) was incorrectly specified as an MPI_INT during a broadcast. Therefore, all non-root processes received a truncated value of this parameter. This simple fix produced the expected behaviour for me.
 2019-06-11 13:48:01 -07:00
Axel Kohlmeyer 1dc8bb163d
Merge pull request #1485 from Adrian-Diaz/memcpy2memmove 
replace some calls to `memcpy()` with calls to `memmove()`
 2019-06-11 14:07:46 -04:00