v0.10.0

CellListMap v0.10.0

Diff since v0.9.17

Version 0.10.0

• Automatic tracking of position mutations and updating of cell lists.
• pairwise!(; reset=[true(default)/false]: the optional reset keyword of pairwise!, when set to false, avoids resetting the initial value of output to zero(typeof(output)).
• update!(sys::AbstractParticleSystem;) as cleaner and more convenient way to update system properties.
• reduce_output! is exposed API for advanced custom reductions.
• Improve scaling of cell list construction and updating.
• Improve performance of inner loops.
• Improve performance of neighborlist reduction and cold start of lists.
• Update list of unchanched coordinates of NonPeriodicCell only if the limits expanded.
• Split computation of NonPeriodicCells into its own path, which then can be simplified. Should display better performance and scalling, particularly in the cell list construction step.
• map_pairwise! was renamed to pairwise!.
• pairwise, without the ! was removed, to stress the fact that the function always mutates the output field of the ParticleSystem object.
• The initial value of output is not set to zero(typeof(output)) by default, but retains the given value. Resetting occurs on the call to pairwise! by default, and can be skipped with reset=false.
• The previous "lower level interface" is now internal and not exported or public anymore.
• The autoswap function was removed, in favor of the new pairwise!(f, x, sys) method. It not available anymore in for neighborlist functions.
• The python interface was currently discontinued.
• validate_coordinates has to be a Function ((x) -> nothing to skip all validation).
• AbstractParticleSystem, ParticleSystem1 and ParticleSystem2 are documented as public, to control dispatch in advanced applications.
• Renamed internal methods of pairwise! to _pairwise! to improve error messages.
• Remove custom linear algebra code, use Base methods.
• Remove deprecated code, improve code coverage.
• Remove internal coordinate swapping by size.
• Internal implementation of neighborlist moved to ParticleSystem interface.
• The internal representation of coordinantes is done with ParticleSystemPositions array type - which is not a subtype of abstract array.
• Add performance test.
• Update examples.
• Default name for output in ParticleSystem is default_output_name, but it can be accessed though sys.output, as before.
• Internal fields of ParticleSystems are not part of PrivateParticleSystemData and are accessed through internal getter functions, or through sys.private.field.
• Fix cross-computation (pairwise!(f, x, sys)) with NonPeriodicCell failing to find pairs when particle coordinates span negative values or large coordinate ranges / do not modify input coordinates in NonPeriodicCell. This bug was never released, it was created and fixed in the development version.
• If the number of particles is reduced by updating and becomes smaller than nbatches, there was a crash. Fixed. Also fixed automatic updating of nbatches when first set of positions change (bug never released).
• Fix nbatches not being updated for the :map phase of CellListPair systems when the particle count changes (bug never released).

Merged pull requests:

• Preview0.10.0 (#144) (@lmiq)
• Clean up code (#145) (@lmiq)
• Optimize parallel cl build (#146) (@lmiq)
• remove redundant work in inner loops (#147) (@lmiq)
• remove custom linear algebra code (#148) (@lmiq)
• Codecov (#149) (@lmiq)
• Public abstractparticlesystem (#150) (@lmiq)
• Remove swap (#151) (@lmiq)
• Non periodic cross bug fix (#152) (@lmiq)
• use ParticleSystemPositions internally to represent coordinates. (#153) (@lmiq)
• Perf regression fix (#154) (@lmiq)
• simplify interface dispatch (#155) (@lmiq)
• View particlepositions (#156) (@lmiq)
• do not change input coordinates in NonPeriodicCell to avoid bad use (#157) (@lmiq)
• Performance test (#158) (@lmiq)
• Nb parallel improvement (#159) (@lmiq)
• List size hint (#160) (@lmiq)
• remove deprecated code (#161) (@lmiq)
• use ShowMethoTesting to rest show methods (#162) (@lmiq)
• update unitcell of unchanged coordinates only if limits expanded (#163) (@lmiq)
• New update! function (#164) (@lmiq)
• fix nbatches update bug, and tiny-system issue of batches (#165) (@lmiq)
• update examples (#166) (@lmiq)
• Non periodic path (#167) (@lmiq)
• Internal vars (#168) (@lmiq)
• set version to 0.10.0 (#169) (@lmiq)

Closed issues:

• Simplify dispatch of UpdateCellList! ? (#58)
• Deprecate autoswap option (#139)

v0.9.17

CellListMap v0.9.17

Diff since v0.9.16

• This version is identical to 0.9.15 - it is being recovered to avoid subtle breaking behaviors introduced in 0.9.16, which might require a breaking release.

v0.9.16

CellListMap v0.9.16

Diff since v0.9.15

Version 0.9.16

• Improve scaling when two sets of particles are used.
• Automatic updating of the number of batches if the number of particles change.
• Some code simplification and add comments to code. Fix documentation typos.
• Drop support for Julia 1.9 (requires 1.10)
• The autoswap option was deprecated, and does not have any effect now. Kept for backwards compatibility.

Merged pull requests:

• Automatic nbatches and new CellListPair construction (#111) (@lmiq)
• Tests and simplifications (#138) (@lmiq)
• set version to 0.9.16 (#140) (@lmiq)

Closed issues:

• Increasing number of batches causes an error in map_pairwise! (#106)
• Bad scaling when 2 sets of particles are used. (#108)

v0.9.15

CellListMap v0.9.15

Diff since v0.9.14

Version 0.9.15

• Better error messages and documentation of unitcell requirements.
• Use julia-actions/cache@v2 in CI

Merged pull requests:

• Refactor CI workflow for caching and permissions (#135) (@lmiq)
• Better error message unitcell (#136) (@lmiq)

v0.9.14

Update image and video links in the documentation.

v0.9.14

CellListMap v0.9.14

Diff since v0.9.13

Version 0.9.14

• Document the fact that the order of the pairs output by neighborlist functions is not guaranteed.

Merged pull requests:

• document order of pairs in neighborlists (#133) (@lmiq)

Closed issues:

• NeighborList Order (#132)

v0.9.13

CellListMap v0.9.13

Diff since v0.9.12

Version 0.9.13

• Document the fact that the unitcell matrix is column-major, thus columns are the lattice vectors.

Merged pull requests:

• Document column major cell (#130) (@lmiq)
• set version to 0.9.13 (#131) (@lmiq)

Closed issues:

• unitcell expects columns or rows? (#129)

v0.9.12

CellListMap v0.9.12

Diff since v0.9.11

Version 0.9.12

• Improve type propagation when no PBCs are used, fixing Float32 to Float64 conversion of sides when unitcell=nothing.
• When no PBCs are defined, and the position limits are smaller than the cutoff, with some pathological coordinates, double-counting could occurr. Fixed.

Merged pull requests:

• Type prop nothing unitcell (#127) (@lmiq)

v0.9.11

CellListMap v0.9.11

Diff since v0.9.10

Version 0.9.11

• Fix typo in color definition of non-interface function draw_computing_cell.
• Reduce precompilation work by running smaller examples
• Add tests to random cells with negative off-diagonal elements.

Merged pull requests:

• test cells with negative values (#120) (@lmiq)
• add changelog and changlog CI (#121) (@lmiq)
• Fix draw computing cell (#123) (@lmiq)

Closed issues:

• Error using "CellListMap.draw_computing_cell" (#122)

v0.9.10

CellListMap v0.9.10

Diff since v0.9.9

• Bump PDBTools compat entry (only used for testing).