Version 2.1.0

SHA256=26c807341502d1ec5f933d72273d89927113fbb8d0366b4b9207552104d10329 (faunus-2.1.0.tar.gz)

• New features

  • starting from this version, we aim to release using semantic versioning
  • tips are given in case of incorrect input. Disable from command line with --notips
  • added akesson mean field correction energy
  • added confid molecular reaction coordinate
  • added qrfile analysis and VMD script for visualising grand canonical ensembles
  • html manual install into share/faunus. Can be launched from shell with faunus-manual.
  • example/test for double-layer in slit geometry
  • example/test for weighted conformational swap moves
  • /usr/bin/env yason.py shebang added to example YAML files to
    automatically convert to JSON when executed. One can thus run
    simulations with ./minimal.yml | faunus

• Fixes and internal changes:

  • compilation passes with -Wall -Wextra -pedantic-errors
  • updated to latest versions of pybind11; nlohmann/json; Eigen
  • fixed random position generation in slit geometry
  • fixed penalty function error when loading from state file
  • bugfix: penalty function broken reference to space particles / molecules
  • anaconda osx: openmpi -> mpich
  • solved travis build timeout issue
  • added Equidistance2DTable for random-access, constant complexity lookup tables
  • added Space::activeParticles() for range-based for loops

Version 2.0.4

• overlap check with non-cuboidal simulation containers
• individual energy terms are timed
• moleculelist: FASTA sequence loader
• pivot: optimised energy evaluation
• bonded: optimisation of energy calculation
• nonbonded: control of OpenMP behaviour
• conda builds with OpenMP on Linux_x64 (not yet on osx)
• added chargemove
• added reactioncoordinate analysis
• added sanity analysis
• new reaction coordinates:
  • atom: charge
  • molecule: COM, number of atoms, net charge, dipole moment, angle, muangle
  • system: radius
• polymers example/test
• improved documentation
• fix translational moves on sphere/disc/line (needed for Dynamic MC)
• multiple minor fixes

Version 2.0.2

• Cluster move: rewritten mass-center routine
• Virtual volume move analysis: fix for numerical overflow error
• Geometries selectable from input (cuboid, slit, sphere, cylinder)
• Documentation update
• py36 and py37 targets in Anaconda (OSX and Linux)
• Multiple minor bugfixes

Version 2.0.1

v2.0.1

conda build name change

Version 2.0-beta.3

Bugfixes, more robust input handling, additional examples.

Version 2.0-beta.2

• many bugfixes
• manual improvements
• speciation examples

Version 2.0 Beta

Re-written version of Faunus, feature incomplete compared to earlier versions. Noticeable differences:

• a single executable, faunus, for running most simulations and tests
• much improved error handling
• a manual! (pdf and online)
• completely re-written internals

Version 1.0.2

Changes since last release:

• chargefile keyword for molecules for overwriting atomic charges
• PowerSASA energy term restored
• Atomic translation now uses a unit sphere instead of a unit cube (important for dynamic MC)

Version 1.0.1

List of changes:

• Capped or "death star" particles
• Widom insertion for molecules
• Multipole analysis, arbitrary multipoles
• Energy matrix for storing old energies
• Improvements to grand canonical salt
• Akesson long range correction
• Tabulated potentials
• Updated documentation
• 2D hypersphere example
• Coulomb Galore pair potential
• Error checks and improved warnings
• Bug fixes

Version 1.0

First release! It's pretty stable, but by no means free from bugs and the interface is as usual pretty rough. Use this over the master branch until next release.