NESSie - v1.5.0

NESSie v1.5.0

Diff since v1.4.5

Merged pull requests: - Base: export _data_path as nessie_data_path (#51) (@tkemmer) - BEM: refactor multithreading, replace thread-local state by tasks (#46) (@tkemmer) - Rjasanow/Radon: add multi-threading support (#45) (@tkemmer) - BEM: enable benchmarking (#44) (@tkemmer) - Base: add GeometryBasics.Rect(model) for bounding box computation (#41) (@tkemmer) - Refactor potential functions, unify interface for BEM and TestModel (#38) (@tkemmer) - Docs: update example code (#37) (@tkemmer) - TestModel: add additional Xie test models (local, second nonlocal) (#36) (@tkemmer) - TestModel: Rename XieModel to XieSphere to avoid confusion with the actual sphere-based test models (#35) (@tkemmer) - Add espotential for electrostatic potentials w/ automatic domain guessing/computation (#34) (@tkemmer) - BEM: add φΓ postprocessor for surface potentials (#33) (@tkemmer) - Base: add guess_domain to locate observation points wrt models (#32) (@tkemmer) - TestModel: remove bornmodel in favor of Model(::BornIon) (#31) (@tkemmer) - Support Model{T, Triangle{T}} generation for test models (#29) (@tkemmer) - Allow abstract strings as string arguments (where possible) (#27) (@tkemmer) - Enable pretty printing for many structs (#26) (@tkemmer) - Refactor molecular potentials, unify interface (#20) (@tkemmer) - Base: deprecate obspoints_line in favor of LinRange (#19) (@tkemmer) - BEM: allow gmres solver options to be modified (#18) (@tkemmer) - TestModel: add bornmodel for built-in models of Born ions (#15) (@tkemmer) - TestModel: include system constants in BornIon, update potentials to use them (#14) (@tkemmer) - Base: move potential functions to main module to avoid clashes (#13) (@tkemmer) - Use AutoHashEquals.jl for many structs (#12) (@tkemmer) - Base: provide GeometryBasics.mesh(model) for triangle mesh conversion (#9) (@tkemmer) - Fix compat lower bounds for Julia 1.12 (#5) (@tkemmer) - Bump minimum supported Julia version to 1.10 LTS (#4) (@tkemmer)

- Julia
Published by github-actions[bot] 7 months ago

NESSie - v1.4.5

NESSie v1.4.5

Diff since v1.4.4

Merged pull requests: - CompatHelper: bump compat for ImplicitArrays to 0.3, (keep existing compat) (#47) (@github-actions[bot]) - Backports v1.4.5 (#48) (@tkemmer)

- Julia
Published by github-actions[bot] 7 months ago

NESSie - v1.4.4

NESSie v1.4.4

Diff since v1.4.3

Merged pull requests: - Backports v1.4.4 (#42) (@tkemmer)

Closed issues: - BEM: type piracy from ImplicitArrays.jl (#43)

- Julia
Published by github-actions[bot] 8 months ago

NESSie - v1.4.3

NESSie v1.4.3

Diff since v1.4.2

Merged pull requests: - Base: fix vertexnormals docstring (#28) (@tkemmer) - BEM: fix multi-threading issues when interactive threads are present (#40) (@tkemmer) - Backports v1.4.3 (#30) (@tkemmer)

Closed issues: - dat caches ignore interactive threads, potentially causing errors in multi-threaded environments (#39)

- Julia
Published by github-actions[bot] 11 months ago

NESSie - v1.4.2

NESSie v1.4.2

Diff since v1.4.1

Merged pull requests: - Backports 1.4.2 (#11) (@tkemmer) - Documentation updates and fixes (#10) (@tkemmer) - Base: fix ∇φmol w/ empty charge lists (#17) (@tkemmer) - Fixes for NonlocalXieModel1 (#25) (@tkemmer)

Closed issues: - Wrong return value/type for ∇φmol w/ empty charge list (#16) - TestModel.scalemodel fails for single-charge systems (#21) - NonlocalXieModel1: origin as observation point yields wrong energies (#22) - NonlocalXieModel1: precomputation of coefficients fails if charges are located in the origin (#23) - NonlocalXieModel1: different born potential definitions used for charges (not) located at the origin (#24)

- Julia
Published by github-actions[bot] 12 months ago

NESSie - v1.4.1

NESSie v1.4.1

Diff since v1.4.0

Merged pull requests: - BEM: use :static scheduling for implicit solvers (#8) (@tkemmer) - Backports v1.4.1 (#6) (@tkemmer)

Closed issues: - Implicit: task migration might corrupt dat caches (#7)

- Julia
Published by github-actions[bot] about 1 year ago

NESSie - v1.4.0

NESSie v1.4.0

Diff since v1.3.3

- Julia
Published by github-actions[bot] over 1 year ago

NESSie - v1.3.3

• BEM: fix explicit nonlocal solver ({BLAS => LinearAlgebra}.axpy!) (2a0ddd0fed025c36cdc184454f380c62f9b00654)

Full Changelog: https://github.com/tkemmer/NESSie.jl/compare/v1.3.2...v1.3.3

- Julia
Published by tkemmer over 1 year ago

NESSie - v1.3.2

• Minor fixes and improvements

Full Changelog: https://github.com/tkemmer/NESSie.jl/compare/v1.3.1...v1.3.2

- Julia
Published by tkemmer over 1 year ago

NESSie - v1.3.1

• BEM: avoid vector/matrix copies in nonlocal solver (777003f94f80abd28c961cdfa5885c482f9a72af)
• BEM: fix ambiguity for matrix multiplication w/ interaction matrices (dc8f811c0a990e8edc0f516d57113d6433e9b6fc)

Full Changelog: https://github.com/tkemmer/NESSie.jl/compare/v1.3.0...v1.3.1

- Julia
Published by tkemmer over 1 year ago

NESSie - v1.3.0

• Greatly reduce the number of required allocations for all solvers (09efee420ccdbaccdf8a300f9d42ee04c3199791, 11c301f8edf46eb3ad7af9a9ab275a888c483687, 0c17e66aad5eddea0339d7e5e27713f4fb9d1122, df4ec694f155cb8982b7c0762fa9a08acd0477f0)
• Add fast dot products and Euclidean distances for 3-element vectors (206cfa01b14976f8db3beae39440c58c136f98d5, 798ce1e9479fe18ef0ca91b55cd929e669f9137f)
• Add writeobj (Wavefront OBJ) support (3a27de1973346e4ef98ae721bae570d57e424e5c, 1f61e8c5bd0b057b7a11e4bbedaf2bf40100c869)
• Move documentation to docs directory (c94fcce1481177cf5e9b6d1c1f90e7e2f724fdbc)
• Extend quadraturepoints to compute points on triangles (af0f6bcda2fd384e5ddb643ed0b50aa63ba6cbc0, 618bfde1ba870a69de3bc0701a5407b91432391b, 3d2deed36cfbbc2f615aad440423d56bab6d6376)
• Make more functions accept abstract arrays (1db7a8afd3f6c7cdf902e643351184080c25aa93, c46c9dfb65be2976b7edab5faf38d655643862af, 5e7462d3bd339d3cf9bfc55def42d2f1be9723f4)
• Use JSON3 instead of JSON (dfb10de97a0c7c83498b741e709d7569540578f2)
• Un-deprecate regularyukawacoll (a2c889479e10a76e7fd0c92f1d41f4333fd6df50)
• Stop pirating Base functions (82fddd8d24a9799ac1c4c17be9708ffdefc97b21, 461ee0c5ca57a0dfcb63458c4c2777478abbad23, 1ce37aaed23861761a5e2d784309342f6da7f4e8, 154e4a639f1b9a04797633099e1746d92459407d)
• Fix vertex orphans in readstl() (e5ca897628001dffc59f8cd726035aec0bbf2f28)
• Fix readback test utility (1b90594e8994978372903610dafef1a266eb1a4f)
• Fix long strings for Julia 1.6 (335604b0907607afec53b0ea137a0935487ddfb2)
• Minor fixes and improvements

Full Changelog: https://github.com/tkemmer/NESSie.jl/compare/v1.2.1...v1.3.0

- Julia
Published by tkemmer about 2 years ago

NESSie - v1.2.2 (EOL)

This is the final release of the v1.2 series. Please upgrade!

• Fix vertex orphans in readstl() (72b2890b5c8f4c4ecb9b20cba03034e3829d7809)
• Fix readback test utility (287bd30ec0a0c25d3a7994ede17fc2d8166564f9)
• Minor fixes and improvements

Full Changelog: https://github.com/tkemmer/NESSie.jl/compare/v1.2.1...v1.2.2

- Julia
Published by tkemmer about 2 years ago

NESSie - v1.2.1

Improvements

• Update compat

Fixes

• Fix left division operation for Julia 1.9

- Julia
Published by tkemmer over 3 years ago

NESSie - v1.2.0

Features

• Local and nonlocal BEM solvers for implicit system representations (solve_implicit)
• Improved Float32 handling
• Surface model import from STL format
• Surface model export to HMO format
• GitHub action for automated documentation builds

Fixes

• Minor fixes and improvements

- Julia
Published by tkemmer over 5 years ago

NESSie - v1.1.1 (EOL)

This is the final release of the v1.1 series. Please upgrade!

Backports from v1.2

• Improved Float32 handling
• GitHub action for automated documentation builds
• Minor fixes and improvements

- Julia
Published by tkemmer over 5 years ago

NESSie - v1.1.0

Features

• Laplace potentials for single observation points and triangles
• Yukawa potentials for single observation points and triangles
• Export surface models to binary STL files
• Converter.jl tool now also supports export to binary STL files
• Charge models generated from PQR files don't include zero-charges anymore
• BEMResult and its subtypes are now exported from the BEM module

Fixes

• Fix nonlocal reaction field energy (post-processing)
• Fix the limit of the regular part of the Yukawa potential's normal derivative
• Minor fixes and improvements

- Julia
Published by tkemmer almost 6 years ago

NESSie - v1.0.3 (EOL)

This is the final release of the v1.0 series. Please upgrade!

• Fix nonlocal reaction field energy (post-processing)
• Fix the limit of the regular part of the Yukawa potential's normal derivative
• Minor improvements

- Julia
Published by tkemmer almost 6 years ago

NESSie - v0.6.2 (EOL)

This is the final release of the v0.6 series! Please upgrade!

• Fix nonlocal reaction field energy (post-processing)
• Fix the limit of the regular part of the Yukawa potential's normal derivative

- Julia
Published by tkemmer almost 6 years ago

NESSie - v1.0.2

• Fix issues with local/nonlocal BEM results introduced when porting to Julia 1.0
• Minor improvements

- Julia
Published by tkemmer about 6 years ago

NESSie - v1.0.1

• Lower required Julia version to 1.0+
• Switch to new Pkg module

- Julia
Published by tkemmer over 6 years ago

NESSie - v0.6.1

• Fix VERSION file for 0.6.* series

- Julia
Published by tkemmer over 6 years ago

NESSie - v1.0

• Support for Julia 1.1

- Julia
Published by tkemmer over 6 years ago

NESSie - v0.6

Original release presented in

Kemmer, T, Rjasanow, S., Hildebrandt, A (2018). NESSie. jl–Efficient and Intuitive Finite Element and Boundary Element Methods for Nonlocal Protein Electrostatics in the Julia Language. Journal of Computational Science 28, 193-203.

Note: This version of NESSie.jl requires Julia v0.6!

- Julia
Published by tkemmer over 6 years ago