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
178eff237b
Merge pull request #520 from stanmoore1/kokkos_update
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Kokkos library update to v2.03.05
2017-06-15 08:47:09 -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
c98bb7fa5f
Corrected minor bug in utility script
2017-06-15 12:57:44 +01:00
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
e7634a44f4
updated thermo_modify in example
2017-06-14 13:11:54 -04:00
3214d639aa
removed unneeded .gitignore
2017-06-14 12:26:52 -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
e139a7fd45
Updated docs for vashishta/gpu
2017-06-14 13:52:03 +02:00
d7646aeeed
Fixed opencl error
2017-06-14 12:03:47 +02:00
5f9341813d
Removed debug output
2017-06-14 10:57:54 +02:00
8441307185
Removed non-general CUDA-dir in makefile
2017-06-14 10:28:46 +02:00
720af5c360
Added vashishta to OpenCL makefile
2017-06-14 10:27:52 +02:00
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
7a05d87f7c
update USER-TALLY examples
2017-06-12 22:20:36 -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
cfeb9b5ba5
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2017-06-12 14:20:50 -04:00
0c805d0b70
correctly skip over point particles and point dipoles when counting extendend particles in fix rigid/small
2017-06-12 14:20:38 -04:00
6b289b0794
change incorrect EINERTIA constant in rigid body integrators from 4.0 to 2.0 (same as in other integrators)
2017-06-12 14:07:40 -04:00
078f2a0a47
Convert/Reindex phir* arrays
2017-06-12 17:41:09 +02:00
bdd908c303
update documentation for USER-MEAMC package and pair style meam/c
2017-06-11 21:54:18 -04:00
b45a95107d
remove ambiguous access conflict to fm_exp() in pair style agni/omp after moving fm_exp() to math_special.h
2017-06-11 18:45:40 -04:00
9f852f5f58
Improve C++-ness, eliminate some macros
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- fm_exp moved to math_special (exp2 was already there)
- use std::min/max template instead of macros
- use memory->create for dynamic arrays (still 1-indexed with macro)
- remove _ from function names, adjust method visibility
2017-06-11 16:55:41 +02:00
fea28d8028
ensure that allocatable_double_2d types are initialized
2017-06-11 07:29:44 -04:00
afed8bb978
make changes to pass compilation test
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- move MEAM class into LAMMPS_NS namespace
- move inclusion of meam.h header to pair_meamc.cpp to reduce namespace pollution
- use forward declaration for MEAM class reference
- make that class reference a pointer and add a destructor
- replace MAX/MIN macros with versions compatible with older compilers
2017-06-11 07:18:13 -04:00
03c93b31d6
Convert to C++, allow multiple instances
2017-06-11 11:29:24 +02:00
d3f31547f9
Reformat code with clang-format (Mozilla style guide)
2017-06-11 11:29:24 +02:00
