Skip to content

Using Linkcells to accelerate the NL #1403

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Iximiel wants to merge 5 commits into
base: master
Choose a base branch
from
+1,084 −71
Open

Using Linkcells to accelerate the NL #1403

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
5203689
adding an mpi-only version of the NL+LC algorithm
Iximiel Apr 20, 2026
aa4dd63
moved the support function into LinkCells
Iximiel May 7, 2026
948aadb
compacting the code in the NL
Iximiel May 7, 2026
a3d87fa
adde a way to toggle the new algorithm
Iximiel May 11, 2026
a262b27
correcting a test
Iximiel May 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions regtest/tools/rt-Neigbourlist-NLLC/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
include ../../scripts/test.make
8 changes: 8 additions & 0 deletions regtest/tools/rt-Neigbourlist-NLLC/config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
mpiprocs=3
type=make
extra_files="../rt-Neigbourlist/main.cpp"

export PLUMED_NUM_THREADS=3

#to test that the new algorithm does not impact the calculations
export PLUMED_FORCE_NL_LC=yes
54 changes: 54 additions & 0 deletions regtest/tools/rt-Neigbourlist-NLLC/testNoNL.reference
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
[NoNL, pbc off] atom 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 1: 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 2: 0 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 3: 0 1 2 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 4: 0 1 2 3 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 5: 0 1 2 3 4 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 6: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 7: 0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 8: 0 1 2 3 4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 9: 0 1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 10: 0 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 11: 0 1 2 3 4 5 6 7 8 9 10 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 12: 0 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 13: 0 1 2 3 4 5 6 7 8 9 10 11 12 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 14: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 15: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 16: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 17: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 18 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 18: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 20 21 22 23 24 25 26
[NoNL, pbc off] atom 19: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25 26
[NoNL, pbc off] atom 20: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 25 26
[NoNL, pbc off] atom 21: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 23 24 25 26
[NoNL, pbc off] atom 22: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 25 26
[NoNL, pbc off] atom 23: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 24 25 26
[NoNL, pbc off] atom 24: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 25 26
[NoNL, pbc off] atom 25: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26
[NoNL, pbc off] atom 26: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[NoNL, pbc on] atom 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 1: 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 2: 0 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 3: 0 1 2 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 4: 0 1 2 3 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 5: 0 1 2 3 4 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 6: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 7: 0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 8: 0 1 2 3 4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 9: 0 1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 10: 0 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 11: 0 1 2 3 4 5 6 7 8 9 10 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 12: 0 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 13: 0 1 2 3 4 5 6 7 8 9 10 11 12 14 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 14: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 15 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 15: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 16: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 17: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 18 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 18: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 20 21 22 23 24 25 26
[NoNL, pbc on] atom 19: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25 26
[NoNL, pbc on] atom 20: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 25 26
[NoNL, pbc on] atom 21: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 23 24 25 26
[NoNL, pbc on] atom 22: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 25 26
[NoNL, pbc on] atom 23: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 24 25 26
[NoNL, pbc on] atom 24: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 25 26
[NoNL, pbc on] atom 25: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26
[NoNL, pbc on] atom 26: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Loading
Loading