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
49e83b4348
patch 21Feb17 sync with GHub
2017-02-21 16:07:26 -07:00
6e89ccd522
Merge pull request #385 from akohlmey/collected-small-bugfixes
...
collected small bugfixes and updates
2017-02-21 15:59:06 -07:00
53f3df5bfc
Merge pull request #384 from lammps/another_neigh_refactor
...
more neighbor list changes, some new options
2017-02-21 15:57:23 -07:00
3dbbea342a
remove a debug print line
2017-02-21 15:57:03 -07:00
b70c670aac
Merge pull request #383 from stanmoore1/rshan_class2_kk
...
Kokkos version of class2 bond, angle, dihedral, and improper from Ray Shan
2017-02-21 15:52:10 -07:00
1d17cae407
Merge pull request #382 from timattox/master_kokkos_neigh_bugfix
...
neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies
2017-02-21 15:51:35 -07:00
429264a12b
Merge pull request #380 from hheenen/core_shell_documentation
...
updated documentation and examples for coreshell
2017-02-21 15:50:53 -07:00
d001a09345
Merge pull request #379 from ndtrung81/pppm-gpu-compute-group-group
...
Fixed bugs with pppm/gpu when used with compute group/group
2017-02-21 15:50:28 -07:00
cb9d42da08
Merge pull request #378 from timattox/USER-DPD_ssa_update
...
USER-DPD: performance optimizations to ssa_update() in fix_shardlow
2017-02-21 15:50:07 -07:00
7185ec92b3
Merge pull request #377 from stanmoore1/kokkos_update
...
Kokkos library update
2017-02-21 15:49:50 -07:00
1cd4c48ccc
new SNAP potential for W
2017-02-21 15:49:21 -07:00
a88136c3f5
correct a logic bug in fix wall/gran/region
2017-02-17 17:58:24 -05:00
ce20c7ffe9
remove debug code
2017-02-17 12:42:07 -05:00
4a80df3a99
more neighbor list changes, some new options
2017-02-15 16:45:33 -07:00
5f93fad012
Add copymode protection to class2 styles
2017-02-15 13:56:16 -07:00
ccaec315db
Updating docs for Kokkos class2
2017-02-15 13:00:33 -07:00
c6c1852b3b
Fix a few issues with Kokkos class2 files
2017-02-15 12:44:54 -07:00
69a8e19dc5
Add files from Ray Shan for Kokkos version of class2 angle, bond, etc.
2017-02-15 12:29:52 -07:00
928947dcea
neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies.
...
This corresponds to a bugfix from commit 9161bd98
2017-02-15 11:49:34 -05:00
48070011d9
update names in example, too
2017-02-14 07:42:36 -05:00
0fb8dacc00
one more Finchham to Fincham change
2017-02-14 07:41:05 -05:00
6b923476b9
updated documentation and examples for coreshell
2017-02-14 13:14:22 +01:00
20806dd86a
Fixed bugs with pppm/gpu when used with compute group/group
2017-02-14 00:26:55 -06:00
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
