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Automatic nbatches #111

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Automatic nbatches #111

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@lmiq lmiq commented Dec 12, 2024 •
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This PR will implement automatic nbatches updating when it is not set manually. Fixes #106.

This PR is a continuation of PR #110

In combination, these PRs will introduce important breaking changes, but significant code and interface simplification.

lmiq added 30 commits December 9, 2024 12:42
@lmiq
refactoring to have both sets with cell lists
c72ba08
@lmiq
use Bool swap instead of type-parameter
7d92ef1
@lmiq
update calls to read_pdb
a868499
@lmiq
restructure data of CellListPair to carry the two cell lists
6ec07c8
@lmiq
loop over cells in CellListPair
580d3ac
@lmiq
fix some calls, remove autoswap
f310e7c
@lmiq
reorganize code and adjust cross inner loop
025a68b
@lmiq
fix indexing of current cell
e0fa83e
@lmiq
fix serial cell indexing
69f8a57
@lmiq
if x coordinates are updated, now we need to update lists
cb54416
@lmiq
add additional tests for resizing
506818a
@lmiq
update doctests
5aedd56
@lmiq
update docs
093e681
@lmiq
update pdbtools compat entry
38ff37c
@lmiq
drop compatibility for Julia < 1.10
19a5f6b
@lmiq
update downgrade CI
58502ad
@lmiq
update downgrade CI
91cec4b
@lmiq
fix doctest for the number of threads run on CI
c57e0a0
@lmiq
update precompiletools compat entry
fe06c95
@lmiq
implement mapping of coordinates to list. Needs testing and updated d…
f560948 
…ocs.
@lmiq
add method to support matrix in new function
a342ff8
@lmiq
renamed internal function
0868571
@lmiq
fix case where particle is outside computing box of target cell list
64a01bd
@lmiq
nicer test for cartesian position of the cell
ac664b6
@lmiq
fix allocation, add some documenation, and a jldoctest
c3f6ff3
@lmiq
add BenchmarkTools to docs project
d7ac3eb
@lmiq
better precompilation setup
2ac7d4e
@lmiq
remove conditional running of precompilation for Julai versions
7171249
@lmiq
add tests for new cross_x_vs_sys function
c211971
@lmiq
add test for output_threaded=nothing
74dbf5f
lmiq added 20 commits December 12, 2024 10:58
@lmiq
add test for output of nbatches
4b6b57c
@lmiq
throw @warn and test setting nbatches with parallel=false
0f0f788
@lmiq
add test for updateing celllistpair with parallel=false
604dae3
@lmiq
add test for internal argument error
1ee4cdd
@lmiq
add additional pathological coordinate and avoid NaN comparison
bcd3087
@lmiq
add tests for show methods
0e1d7de
@lmiq
throw message for test_show changed
83b24cf
@lmiq
document new single-cell list cross interaction method
4bc6047
@lmiq
starting implementing automatic nbatches updating
92e95f4
@lmiq
update structure and updating scheme of nbatches (WIP)
a3a806d
@lmiq
fix nbatches initialization
4a7ee10
@lmiq
define nbatches for particle systems
9aff819
@lmiq
run CI with 10 julia threads for better testing
f56b7fe
@lmiq
split set and update number of batches
9e63707
@lmiq
fix karg forwarding
bf01912
@lmiq
fix signature of update number of batches for CellListPair
b1aa831
@lmiq
initialize default value for _nbatches
924fe92
@lmiq
fix initialization of batches for CellListPair
d6b479d
@lmiq
fix doctest
9f06c0a
@lmiq
remove testitem block
195e606
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Increasing number of batches causes an error in map_pairwise!
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@lmiq