e129f18e6f
Merge pull request #530 from akohlmey/no_static_sort_in_dump
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Refactor Dump and Irregular classes to remove static class members
2017-06-20 07:43:49 -06:00
8c54fcd1b6
cleanup from aidan for fix reax/c/species and its KOKKOS version
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this version eliminates the need for the PBCconnected list and avoids having to access the spec_atom array for ghost atoms
2017-06-19 17:31:54 -04:00
67a0183b33
Removing atom2bin change since ssa neighlists aren't be used for occasional lists
2017-06-19 15:23:33 -06:00
f5047ac3c7
augment fix shardlow check for ordering fixes to be KOKKOS compatible
2017-06-19 17:23:23 -04:00
b96b6b9cd7
Fixing error checks
2017-06-19 14:04:16 -06:00
164cedf353
protect all OpenMP pragmas with ifdefs and add special conditions for nvcc to ignore unsupported directives
2017-06-19 15:31:20 -04:00
3c329d1707
massive whitespace cleanup in USER-INTEL
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removed are:
- DOS/Windows text format carriage return characters (^M)
- tabs replaced with spaces (tabs are evil!!)
- trailing whitespace
2017-06-19 13:23:01 -04:00
b687d16177
insert C++ file format indicator comments
2017-06-19 13:03:23 -04:00
da0dcbe0bb
Updating to master
2017-06-19 10:56:24 -06:00
8988b692a3
modified the documentation, first and last freeend can have different spring constants
2017-06-19 16:30:42 +02:00
c97415aefa
corrected the initial free end
2017-06-19 14:57:39 +02:00
a9f3f90025
fix uninitialized members
2017-06-19 12:51:18 +02:00
9b8de3ba29
remove ifdefs for selecting between plain and hybrid merge sort. use hybrid only.
2017-06-17 09:30:41 -04:00
9b9f6d6fe2
USER-INTEL upgrade from M Brown
2017-06-16 16:56:28 -06:00
c1b0b1b3f9
restore old qsort() based code and add preprocessor directives to switch
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-DLMP_USE_LIBC_QSORT will use qsort() from libc to sort (requires static/global variables).
-DLMP_USE_MERGE_SORT will use a plain merge sort. slightly slower for expensive comparisons.
-DLMP_USE_HYBRID_SORT will use hybrid merge sort. faster than merge sort (no static/global variables)
2017-06-16 18:17:48 -04:00
2a6f026853
mergesort performance improvements
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- use insertion sort to pre-sort data in 32-element chunks
- swap pointers between merge runs instead of copying the data
2017-06-16 08:05:55 -04:00
8728a8ddae
restore heuristics for checking against integrators that broke after PR #499 was merged
2017-06-15 15:16:50 -04:00
9aa450b832
Merge pull request #528 from akohlmey/no_static_in_ring_comm
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Refactor ring communication to no longer require static class variables
2017-06-15 11:13:07 -06:00
0588c382f0
Merge pull request #513 from v0i0/bugfix-airebo-nconj-kronecker
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Bugfix in AIREBO as reported in #59 by @KammIma
2017-06-15 11:12:29 -06:00
d3c90f3c14
Merge pull request #510 from akohlmey/collected-small-changes
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Collected small changes
2017-06-15 11:12:14 -06:00
b62d526cc9
Revert "avoid undesired negative forces for high particle velocities in granular models"
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This reverts commit 066123007c
2017-06-15 11:01:36 -04:00
1a29048940
Merge pull request #531 from ohenrich/user-cgdna
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Affiliation Update for USER-CGDNA
2017-06-15 08:54:52 -06:00
0a6b3f8790
Merge pull request #527 from dstelter92/master
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Added compute_scalar to fix_grem
2017-06-15 08:54:22 -06:00
7227bc415d
Merge pull request #526 from andeplane/vashishta_gpu
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Implemented pair style vashishta in GPU package
2017-06-15 08:52:13 -06:00
a4bc233d86
Merge pull request #525 from akohlmey/user-tally-refactor
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Refactoring of USER-TALLY computes to handle sparse/hybrid system for many processors plus bugfixes
2017-06-15 08:51:24 -06:00
5c5b4ffadb
Merge pull request #522 from akohlmey/tip4p-cleanup-refactor
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Refactor and bugfix for some TIP4P pair styles
2017-06-15 08:48:52 -06:00
30177c4eae
Merge pull request #521 from pastewka/17_dump_nc
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Updated NetCDF dump style (dump netcdf)
2017-06-15 08:47:29 -06:00
576b7f1d97
Merge pull request #519 from Pakketeretet2/USER-MANIFOLD-gaussian-bump
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Some extensions/cleanup in USER-MANIFOLD
2017-06-15 08:46:55 -06:00
86369fec6b
Merge pull request #517 from akohlmey/select-rigid-reinit-option
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Add `reinit` keyword to rigid body fixes
2017-06-15 08:46:29 -06:00
79341ac5d1
Merge pull request #516 from akohlmey/check-rigid-overlap
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Implement check whether commands or styles try to change cached properties in rigid body integrators
2017-06-15 08:44:05 -06:00
66945294a9
Merge pull request #515 from stanmoore1/remove_fences
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Remove unnecessary thread fences in Kokkos package
2017-06-15 08:40:43 -06:00
9a7207e34c
Merge pull request #511 from akohlmey/add-compute-cnp
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Integrate compute cnp/atom contributed by Paulo Branicio (USC)
2017-06-15 08:38:05 -06:00
d41c617d1d
Merge pull request #509 from akohlmey/add-atomonly-npair-for-omp
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add "atomonly" optimized neighbor list build styles to USER-OMP
2017-06-15 08:24:44 -06:00
1ec9e588ff
Merge pull request #504 from andeplane/hexorder_fix
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Using correct ndegree instead of nnn
2017-06-15 08:24:25 -06:00
3c7417fb59
Merge pull request #497 from lammps/add-user-reaxc-omp
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Add USER-OMP compatible OpenMP support to USER-REAXC
2017-06-15 08:24:03 -06:00
34cfc7bd51
Merge pull request #490 from EmileMaras/NEB-Change
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added several features to the NEB
2017-06-15 08:23:04 -06:00
77ca68a2b4
Changed affiliation
2017-06-15 12:52:19 +01:00
06fe703eed
add missing mergesort header
2017-06-14 23:22:49 -04:00
8500a197ae
whitespace cleanup
2017-06-14 23:13:10 -04:00
1f17e8ebbb
remove need for static class member variables in Dump and Irregular
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The dump and irregular classes were using qsort() from the C-library
for sorting lists through custom comparison functions, which required
access to additional data, which was passed via static class variables,
i.e. globals. This collides with having multiple LAMMPS instances in
the same address space.
the calls to qsort() are replaced with a custom merge sort, which passes
a void pointer to the comparison functions, which can contain any kind
of desired information, e.g. a class handle or a list
2017-06-14 23:10:53 -04:00
fcc387f232
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
0ad66ecb89
Added compute_scalar to fix_grem for easier output managment, updated example to show use
2017-06-14 12:18:22 -04:00
eeff0b8633
Added vashishta GPU package for NVidia
2017-06-14 10:24:16 +02:00
32b967ed9c
add rigid body overlap warnings to change_box and delete_atoms
2017-06-13 16:26:49 -04:00
3d066283b6
fix compilation, move meam_cleanup to destructor
2017-06-13 19:41:29 +02:00
29e60fa53a
Move rho/gamma arrays to fields of MEAM, remove arguments and arrdim macros
2017-06-13 18:39:40 +02:00
11751521e7
remove dead code
2017-06-12 22:49:31 -04:00
b01143102d
refactoring of USER-TALLY computes to handle sparse and hybrid systems
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with sparse and hybrid systems, Pair::ev_tally() may not be called on
every processor and thus the computes in USER-TALLY may hang during
reverse communication because of the error->all() call after checking
whether callback from Pair::ev_tally() has been called at least once.
To address this cleanly, a second callback function needs to be added,
which is run during Pair::ev_setup() and will now handle all memory
re-allocation and clearing of accumulators, just like it is done for
regular tallied data.
2017-06-12 22:12:12 -04:00
e530ba46f4
cleanup and bugfix for compute heat/flux/tally
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- make heatj a pointer instead of a static array
- fix memory leaks for eatom, stress
- simplify and streamline computation
2017-06-12 21:46:00 -04:00
420db44596
print incompatible pair style warnings in USER-TALLY only on MPI rank 0
2017-06-12 20:05:15 -04:00
