jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
13,973 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

13973 Commits

Author SHA1 Message Date
smoore 9e35e76b8c Fix issues in Kokkos npair_halffull and npair_skip 2018-01-13 21:32:59 -07:00
Stan Moore 52d3e98f3b Fix issue in npair_skip_kokkos 2018-01-12 15:45:24 -07:00
Stan Moore 6e3acce3be Relax restriction in neighbor.cpp 2018-01-12 15:44:11 -07:00
Stan Moore 1ec54827d6 Add Kokkos halffull neighbor list capability 2018-01-12 15:41:59 -07:00
Stan Moore 45674e6cd3 Add Kokkos skip list capability 2018-01-11 10:07:44 -07:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Steve Plimpton 9e9cfe5869
Merge pull request #754 from rbberger/cmake_kokkos_bugfix 
CMake bugfixes for KOKKOS builds
 2018-01-08 09:16:43 -07:00
Steve Plimpton 85ff0c1e46
Merge pull request #750 from stanmoore1/kk_fences 
Add Kokkos thread fences to comm pack/unpack routines
 2018-01-08 09:16:16 -07:00
Steve Plimpton cc9b6118b8
Merge pull request #748 from stanmoore1/kk_docs 
Update Kokkos docs
 2018-01-08 09:15:36 -07:00
Steve Plimpton 09bed0c09a
Merge pull request #747 from stanmoore1/kk_reax_hist 
Fix broken charge history in fix qeq/reax/kk
 2018-01-08 09:15:21 -07:00
Steve Plimpton 1b51efd6b8
Merge pull request #744 from akohlmey/doc-update 
Documentation build updates
 2018-01-08 09:15:02 -07:00
Steve Plimpton 8888b05b18
Merge pull request #742 from rbberger/fix_python_move 
Fix python/move
 2018-01-08 09:14:36 -07:00
Steve Plimpton 3bb8294f31
Merge pull request #718 from timattox/USER-DPD_es_RNG 
USER-DPD: External State RNG
 2018-01-08 09:13:11 -07:00
Steve Plimpton 450c689ae9
Merge pull request #725 from stanmoore1/kk_update 
Update the Kokkos library in LAMMPS to v2.5.00
 2018-01-08 09:12:51 -07:00
Axel Kohlmeyer 09ca7b32fc Revert "no need to include library.o in the LAMMPS executable" 
This reverts commit 4a3a6b4455.
As it turns out, when using the LAMMPS python wrapper from inside
code using the PYTHON package, the library symbols *are* needed.
Thanks for Richard Berger (@rbberger) for pointing this out.
 2018-01-06 19:47:33 +01:00
Axel Kohlmeyer 3af389e6cf Revert "no need to include library.o in the LAMMPS executable" 
This reverts commit 4a3a6b4455.
As it turns out, when using the LAMMPS python wrapper from inside
code using the PYTHON package, the library symbols *are* needed.
Thanks for Richard Berger (@rbberger) for pointing this out.
 2018-01-06 12:58:17 -05:00
Axel Kohlmeyer 46217db8a5 make python functions examples more complete by adding exception handling and initializing variables 2018-01-06 12:56:42 -05:00
Richard Berger d6d7dde653 Add error output if python evaluation failed 2018-01-06 18:54:55 +01:00
Axel Kohlmeyer 6070182f06 correctly account for individually added bonds, angles, and dihedrals 2018-01-06 11:03:48 -05:00
Axel Kohlmeyer 6c058fb56c avoid division by zero in ewald for empty and uncharged systems. require kspace_modify gewald 2018-01-05 20:14:25 -05:00
Axel Kohlmeyer 91993b236d avoid division by zero in PPPM for empty and uncharged systems. require kspace_modify gewald 2018-01-05 19:52:51 -05:00
Axel Kohlmeyer 5ecc3ce366 avoid division by zero when trying to run PPPM on a system without atoms 2018-01-04 20:44:40 -05:00
Axel Kohlmeyer 75f1a4f3f0 use filelink.o consistently, since filelink does not work with some compilers, e.g. nvcc 2018-01-04 20:43:53 -05:00
Axel Kohlmeyer ffc74fca6c Merge branch 'fix_property_atom_doc_update' of https://github.com/Pakketeretet2/lammps into collected-bugfixes-and-updates 
this closes PR #755
 2018-01-04 19:46:31 -05:00
Axel Kohlmeyer 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
Stefan Paquay c333401e72 Use bold font instead of underscores for emphasis. 2017-12-25 13:27:14 +01:00
Stefan Paquay a9e9a2046b Fixes/clarifies the fix_property_atom docs. 2017-12-25 13:03:18 +01:00
Axel Kohlmeyer d4f45f4f85 correct set command example in fix property/atom 2017-12-24 17:45:58 -05:00
Stan Moore 7d07baa8ad Better load balance fix_qeq_reax_kokkos for half neigh list 2017-12-21 11:07:51 -07:00
Richard Berger b9184ef441 Add special KOKKOS styles individually 
This avoids unnecessary dependencies
 2017-12-20 04:51:46 -05:00
Richard Berger ff2b61354d Bugfix for building LAMMPS+KOKKOS+DPD with CMake 
Resolves issue #753, but there might be more work ahead.
 2017-12-20 03:17:40 -05:00
Axel Kohlmeyer 18acc6ae47 remove some dead code 2017-12-19 15:01:11 -05:00
Axel Kohlmeyer 56e633a2cf error out on trying to compile USER-INTEL with -DLAMMPS_BIGBIG 2017-12-19 14:54:35 -05:00
Stan Moore 798d68c607 Edits to accelerate_kokkos.txt 2017-12-18 14:50:33 -07:00
Stan Moore 46fe0a968b Fix compiler warnings in atom_vec_hybrid_kokkos 2017-12-18 14:09:39 -07:00
Stan Moore 00a9672524 Fix issue in fix_qeq_reax_kokkos, can't call child function from base constructor 2017-12-18 13:58:37 -07:00
Stan Moore a2756db66b Update to Kokkos library v2.5.00 2017-12-15 16:42:06 -07:00
Stan Moore da83feb8ca Merge branch 'master' into kk_update 2017-12-15 16:36:21 -07:00
Stan Moore a7bc3ed391 Add missing fences in comm_kokkos 2017-12-15 13:30:17 -07:00
Stan Moore 68cf6941e1 Add Kokkos thread fences to pack/unpack routines 2017-12-15 13:01:38 -07:00
Richard Berger 73c55ac4d1 Fix up docs after renaming 2017-12-15 14:06:16 -05:00
Richard Berger 2a131d1416 Merge remote-tracking branch 'upstream/master' into fix_python_move 2017-12-15 13:56:54 -05:00
Richard Berger bcc5f49d0b Rename fix python to fix python/invoke 2017-12-15 13:53:04 -05:00
Richard Berger 950bfb84a9 Clean up after renaming back to fix python/move 2017-12-15 13:27:27 -05:00
Richard Berger 4d725c3153 Revert "Rename fix python/move to move/python" 
This reverts commit 4d915dba08.
 2017-12-15 13:17:12 -05:00
Axel Kohlmeyer 10fa54b2fd correct error messages. the atom style is called "smd" not "tlsph" 2017-12-13 18:44:31 -05:00
Axel Kohlmeyer 8a36cdc6bc correct velocity output for write_data of atom style smd 2017-12-13 18:42:24 -05:00
Axel Kohlmeyer e5cd068cd5 Merge branch 'patch-3' of https://github.com/abbatux/lammps into collected-bugfixes-and-updates 
This closes #745
 2017-12-13 17:41:00 -05:00
Axel Kohlmeyer cec22dda92 change pair style airebo/intel to compile with -DLAMMPS_BIGBIG 2017-12-13 16:20:49 -05:00
Axel Kohlmeyer 9a71efc5d5 fix neb bugfix from Emile Maras 
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